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Chen X, Yang W, Roberts CWM, Zhang J. Developmental origins shape the paediatric cancer genome. Nat Rev Cancer 2024; 24:382-398. [PMID: 38698126 DOI: 10.1038/s41568-024-00684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 05/05/2024]
Abstract
In the past two decades, technological advances have brought unprecedented insights into the paediatric cancer genome revealing characteristics distinct from those of adult cancer. Originating from developing tissues, paediatric cancers generally have low mutation burden and are driven by variants that disrupt the transcriptional activity, chromatin state, non-coding cis-regulatory regions and other biological functions. Within each tumour, there are multiple populations of cells with varying states, and the lineages of some can be tracked to their fetal origins. Genome-wide genetic screening has identified vulnerabilities associated with both the cell of origin and transcription deregulation in paediatric cancer, which have become a valuable resource for designing new therapeutic approaches including those for small molecules, immunotherapy and targeted protein degradation. In this Review, we present recent findings on these facets of paediatric cancer from a pan-cancer perspective and provide an outlook on future investigations.
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Affiliation(s)
- Xiaolong Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wentao Yang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Comprehensive Cancer Center, St Jude Children's Research Hospital, Memphis, TN, USA
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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2
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Pomaville M, Chennakesavalu M, Wang P, Jiang Z, Sun HL, Ren P, Borchert R, Gupta V, Ye C, Ge R, Zhu Z, Brodnik M, Zhong Y, Moore K, Salwen H, George RE, Krajewska M, Chlenski A, Applebaum MA, He C, Cohn SL. Small-molecule inhibition of the METTL3/METTL14 complex suppresses neuroblastoma tumor growth and promotes differentiation. Cell Rep 2024; 43:114165. [PMID: 38691450 DOI: 10.1016/j.celrep.2024.114165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/10/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024] Open
Abstract
The N6-methyladenosine (m6A) RNA modification is an important regulator of gene expression. m6A is deposited by a methyltransferase complex that includes methyltransferase-like 3 (METTL3) and methyltransferase-like 14 (METTL14). High levels of METTL3/METTL14 drive the growth of many types of adult cancer, and METTL3/METTL14 inhibitors are emerging as new anticancer agents. However, little is known about the m6A epitranscriptome or the role of the METTL3/METTL14 complex in neuroblastoma, a common pediatric cancer. Here, we show that METTL3 knockdown or pharmacologic inhibition with the small molecule STM2457 leads to reduced neuroblastoma cell proliferation and increased differentiation. These changes in neuroblastoma phenotype are associated with decreased m6A deposition on transcripts involved in nervous system development and neuronal differentiation, with increased stability of target mRNAs. In preclinical studies, STM2457 treatment suppresses the growth of neuroblastoma tumors in vivo. Together, these results support the potential of METTL3/METTL14 complex inhibition as a therapeutic strategy against neuroblastoma.
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Affiliation(s)
- Monica Pomaville
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | | | - Pingluan Wang
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Zhiwei Jiang
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Hui-Lung Sun
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Peizhe Ren
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Ryan Borchert
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Varsha Gupta
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Chang Ye
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Ruiqi Ge
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Zhongyu Zhu
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Mallory Brodnik
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Yuhao Zhong
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Kelley Moore
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Helen Salwen
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Rani E George
- Department of Pediatric Hematology/Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Malgorzata Krajewska
- School of Biochemistry and Cell Biology, Biosciences Institute, University College Cork, Cork, Ireland
| | - Alexandre Chlenski
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Mark A Applebaum
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, University of Chicago, Chicago, Il 60637 USA
| | - Susan L Cohn
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA.
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3
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Pastori V, Zambanini G, Citterio E, Weiss T, Nakamura Y, Cantù C, Ronchi AE. Transcriptional repression of the oncofetal LIN28B gene by the transcription factor SOX6. Sci Rep 2024; 14:10287. [PMID: 38704454 PMCID: PMC11069503 DOI: 10.1038/s41598-024-60438-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
The identification of regulatory networks contributing to fetal/adult gene expression switches is a major challenge in developmental biology and key to understand the aberrant proliferation of cancer cells, which often reactivate fetal oncogenes. One key example is represented by the developmental gene LIN28B, whose aberrant reactivation in adult tissues promotes tumor initiation and progression. Despite the prominent role of LIN28B in development and cancer, the mechanisms of its transcriptional regulation are largely unknown. Here, by using quantitative RT-PCR and single cell RNA sequencing data, we show that in erythropoiesis the expression of the transcription factor SOX6 matched a sharp decline of LIN28B mRNA during human embryo/fetal to adult globin switching. SOX6 overexpression repressed LIN28B not only in a panel of fetal-like erythroid cells (K562, HEL and HUDEP1; ≈92% p < 0.0001, 54% p = 0.0009 and ≈60% p < 0.0001 reduction, respectively), but also in hepatoblastoma HepG2 and neuroblastoma SH-SY5H cells (≈99% p < 0.0001 and ≈59% p < 0.0001 reduction, respectively). SOX6-mediated repression caused downregulation of the LIN28B/Let-7 targets, including MYC and IGF2BP1, and rapidly blocks cell proliferation. Mechanistically, Lin28B repression is accompanied by SOX6 physical binding within its locus, suggesting a direct mechanism of LIN28B downregulation that might contribute to the fetal/adult erythropoietic transition and restrict cancer proliferation.
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Affiliation(s)
- Valentina Pastori
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Gianluca Zambanini
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
- Max-Planck-Institut für molekulare Genetik, Berlin, Germany
| | - Elisabetta Citterio
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Tamina Weiss
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Yukio Nakamura
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Antonella Ellena Ronchi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy.
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4
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Saldana-Guerrero IM, Montano-Gutierrez LF, Boswell K, Hafemeister C, Poon E, Shaw LE, Stavish D, Lea RA, Wernig-Zorc S, Bozsaky E, Fetahu IS, Zoescher P, Pötschger U, Bernkopf M, Wenninger-Weinzierl A, Sturtzel C, Souilhol C, Tarelli S, Shoeb MR, Bozatzi P, Rados M, Guarini M, Buri MC, Weninger W, Putz EM, Huang M, Ladenstein R, Andrews PW, Barbaric I, Cresswell GD, Bryant HE, Distel M, Chesler L, Taschner-Mandl S, Farlik M, Tsakiridis A, Halbritter F. A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations. Nat Commun 2024; 15:3745. [PMID: 38702304 PMCID: PMC11068915 DOI: 10.1038/s41467-024-47945-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
Early childhood tumours arise from transformed embryonic cells, which often carry large copy number alterations (CNA). However, it remains unclear how CNAs contribute to embryonic tumourigenesis due to a lack of suitable models. Here we employ female human embryonic stem cell (hESC) differentiation and single-cell transcriptome and epigenome analysis to assess the effects of chromosome 17q/1q gains, which are prevalent in the embryonal tumour neuroblastoma (NB). We show that CNAs impair the specification of trunk neural crest (NC) cells and their sympathoadrenal derivatives, the putative cells-of-origin of NB. This effect is exacerbated upon overexpression of MYCN, whose amplification co-occurs with CNAs in NB. Moreover, CNAs potentiate the pro-tumourigenic effects of MYCN and mutant NC cells resemble NB cells in tumours. These changes correlate with a stepwise aberration of developmental transcription factor networks. Together, our results sketch a mechanistic framework for the CNA-driven initiation of embryonal tumours.
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Affiliation(s)
- Ingrid M Saldana-Guerrero
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
- Sheffield Institute for Nucleic Acids (SInFoNiA), School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | | | - Katy Boswell
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | | | - Evon Poon
- Division of Clinical Studies, The Institute of Cancer Research (ICR) & Royal Marsden NHS Trust, London, UK
| | - Lisa E Shaw
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Dylan Stavish
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Rebecca A Lea
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Sara Wernig-Zorc
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Eva Bozsaky
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Irfete S Fetahu
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Medical University of Vienna, Department of Neurology, Division of Neuropathology and Neurochemistry, Vienna, Austria
| | - Peter Zoescher
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ulrike Pötschger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Marie Bernkopf
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik GmbH, Vienna, Austria
| | | | - Caterina Sturtzel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Celine Souilhol
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
- Biomolecular Sciences Research Centre, Department of Biosciences and Chemistry, Sheffield Hallam University, Sheffield, UK
| | - Sophia Tarelli
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Mohamed R Shoeb
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Polyxeni Bozatzi
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Magdalena Rados
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Maria Guarini
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Michelle C Buri
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Eva M Putz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Miller Huang
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ruth Ladenstein
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Peter W Andrews
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | | | - Helen E Bryant
- Sheffield Institute for Nucleic Acids (SInFoNiA), School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Martin Distel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research (ICR) & Royal Marsden NHS Trust, London, UK
| | | | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Anestis Tsakiridis
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK.
- Neuroscience Institute, The University of Sheffield, Sheffield, UK.
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5
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Wang J, Hong M, Cheng Y, Wang X, Li D, Chen G, Bao B, Song J, Du X, Yang C, Zheng L, Tong Q. Targeting c-Myc transactivation by LMNA inhibits tRNA processing essential for malate-aspartate shuttle and tumour progression. Clin Transl Med 2024; 14:e1680. [PMID: 38769668 PMCID: PMC11106511 DOI: 10.1002/ctm2.1680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 03/28/2024] [Accepted: 04/19/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND A series of studies have demonstrated the emerging involvement of transfer RNA (tRNA) processing during the progression of tumours. Nevertheless, the roles and regulating mechanisms of tRNA processing genes in neuroblastoma (NB), the prevalent malignant tumour outside the brain in children, are yet unknown. METHODS Analysis of multi-omics results was conducted to identify crucial regulators of downstream tRNA processing genes. Co-immunoprecipitation and mass spectrometry methods were utilised to measure interaction between proteins. The impact of transcriptional regulators on expression of downstream genes was measured by dual-luciferase reporter, chromatin immunoprecipitation, western blotting and real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR) methods. Studies have been conducted to reveal impact and mechanisms of transcriptional regulators on biological processes of NB. Survival differences were analysed using the log-rank test. RESULTS c-Myc was identified as a transcription factor driving tRNA processing gene expression and subsequent malate-aspartate shuttle (MAS) in NB cells. Mechanistically, c-Myc directly promoted the expression of glutamyl-prolyl-tRNA synthetase (EPRS) and leucyl-tRNA synthetase (LARS), resulting in translational up-regulation of glutamic-oxaloacetic transaminase 1 (GOT1) as well as malate dehydrogenase 1 (MDH1) via inhibiting general control nonrepressed 2 or activating mechanistic target of rapamycin signalling. Meanwhile, lamin A (LMNA) inhibited c-Myc transactivation via physical interaction, leading to suppression of MAS, aerobic glycolysis, tumourigenesis and aggressiveness. Pre-clinically, lobeline was discovered as a LMNA-binding compound to facilitate its interaction with c-Myc, which inhibited aminoacyl-tRNA synthetase expression, MAS and tumour progression of NB, as well as growth of organoid derived from c-Myc knock-in mice. Low levels of LMNA or elevated expression of c-Myc, EPRS, LARS, GOT1 or MDH1 were linked to a worse outcome and a shorter survival time of clinical NB patients. CONCLUSIONS These results suggest that targeting c-Myc transactivation by LMNA inhibits tRNA processing essential for MAS and tumour progression.
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Affiliation(s)
- Jianqun Wang
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Mei Hong
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Yang Cheng
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Xiaojing Wang
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
- Department of GeriatricsUnion Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhanHubei ProvinceChina
| | - Dan Li
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Guo Chen
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Banghe Bao
- Department of PathologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Jiyu Song
- Department of PathologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Xinyi Du
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Chunhui Yang
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Liduan Zheng
- Department of PathologyUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
| | - Qiangsong Tong
- Department of Pediatric SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei ProvinceP. R. China
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6
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Chapple RH, Liu X, Natarajan S, Alexander MIM, Kim Y, Patel AG, LaFlamme CW, Pan M, Wright WC, Lee HM, Zhang Y, Lu M, Koo SC, Long C, Harper J, Savage C, Johnson MD, Confer T, Akers WJ, Dyer MA, Sheppard H, Easton J, Geeleher P. An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.13.536639. [PMID: 38712039 PMCID: PMC11071300 DOI: 10.1101/2023.04.13.536639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Neuroblastoma is a common pediatric cancer, where preclinical studies suggest that a mesenchymal-like gene expression program contributes to chemotherapy resistance. However, clinical outcomes remain poor, implying we need a better understanding of the relationship between patient tumor heterogeneity and preclinical models. Here, we generated single-cell RNA-seq maps of neuroblastoma cell lines, patient-derived xenograft models (PDX), and a genetically engineered mouse model (GEMM). We developed an unsupervised machine learning approach ('automatic consensus nonnegative matrix factorization' (acNMF)) to compare the gene expression programs found in preclinical models to a large cohort of patient tumors. We confirmed a weakly expressed, mesenchymal-like program in otherwise adrenergic cancer cells in some pre-treated high-risk patient tumors, but this appears distinct from the presumptive drug-resistance mesenchymal programs evident in cell lines. Surprisingly however, this weak-mesenchymal-like program was maintained in PDX and could be chemotherapy-induced in our GEMM after only 24 hours, suggesting an uncharacterized therapy-escape mechanism. Collectively, our findings improve the understanding of how neuroblastoma patient tumor heterogeneity is reflected in preclinical models, provides a comprehensive integrated resource, and a generalizable set of computational methodologies for the joint analysis of clinical and pre-clinical single-cell RNA-seq datasets.
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7
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Singh S, Fang J, Jin H, Van de Velde LA, Wu Q, Cortes A, Morton CL, Woolard MA, Quarni W, Steele JA, Connelly JP, He L, Thorne R, Turner G, Confer T, Johnson M, Caufield WV, Freeman BB, Lockey T, Pruett-Miller SM, Wang R, Davidoff AM, Thomas PG, Yang J. RBM39 degrader invigorates natural killer cells to eradicate neuroblastoma despite cancer cell plasticity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586157. [PMID: 38585889 PMCID: PMC10996557 DOI: 10.1101/2024.03.21.586157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The cellular plasticity of neuroblastoma is defined by a mixture of two major cell states, adrenergic (ADRN) and mesenchymal (MES), which may contribute to therapy resistance. However, how neuroblastoma cells switch cellular states during therapy remains largely unknown and how to eradicate neuroblastoma regardless of their cell states is a clinical challenge. To better understand the lineage switch of neuroblastoma in chemoresistance, we comprehensively defined the transcriptomic and epigenetic map of ADRN and MES types of neuroblastomas using human and murine models treated with indisulam, a selective RBM39 degrader. We showed that cancer cells not only undergo a bidirectional switch between ADRN and MES states, but also acquire additional cellular states, reminiscent of the developmental pliancy of neural crest cells. The lineage alterations are coupled with epigenetic reprogramming and dependency switch of lineage-specific transcription factors, epigenetic modifiers and targetable kinases. Through targeting RNA splicing, indisulam induces an inflammatory tumor microenvironment and enhances anticancer activity of natural killer cells. The combination of indisulam with anti-GD2 immunotherapy results in a durable, complete response in high-risk transgenic neuroblastoma models, providing an innovative, rational therapeutic approach to eradicate tumor cells regardless of their potential to switch cell states.
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8
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Wang T, Liu L, Fang J, Jin H, Natarajan S, Sheppard H, Lu M, Turner G, Confer T, Johnson M, Steinberg J, Ha L, Yadak N, Jain R, Picketts DJ, Ma X, Murphy A, Davidoff AM, Glazer ES, Easton J, Chen X, Wang R, Yang J. Conditional c-MYC activation in catecholaminergic cells drives distinct neuroendocrine tumors: neuroblastoma vs somatostatinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584622. [PMID: 38559042 PMCID: PMC10980015 DOI: 10.1101/2024.03.12.584622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The MYC proto-oncogenes (c-MYC, MYCN , MYCL ) are among the most deregulated oncogenic drivers in human malignancies including high-risk neuroblastoma, 50% of which are MYCN -amplified. Genetically engineered mouse models (GEMMs) based on the MYCN transgene have greatly expanded the understanding of neuroblastoma biology and are powerful tools for testing new therapies. However, a lack of c-MYC-driven GEMMs has hampered the ability to better understand mechanisms of neuroblastoma oncogenesis and therapy development given that c-MYC is also an important driver of many high-risk neuroblastomas. In this study, we report two transgenic murine neuroendocrine models driven by conditional c-MYC induction in tyrosine hydroxylase (Th) and dopamine β-hydroxylase (Dbh)-expressing cells. c-MYC induction in Th-expressing cells leads to a preponderance of Pdx1 + somatostatinomas, a type of pancreatic neuroendocrine tumor (PNET), resembling human somatostatinoma with highly expressed gene signatures of δ cells and potassium channels. In contrast, c-MYC induction in Dbh-expressing cells leads to onset of neuroblastomas, showing a better transforming capacity than MYCN in a comparable C57BL/6 genetic background. The c-MYC murine neuroblastoma tumors recapitulate the pathologic and genetic features of human neuroblastoma, express GD2, and respond to anti-GD2 immunotherapy. This model also responds to DFMO, an FDA-approved inhibitor targeting ODC1, which is a known MYC transcriptional target. Thus, establishing c-MYC-overexpressing GEMMs resulted in different but related tumor types depending on the targeted cell and provide useful tools for testing immunotherapies and targeted therapies for these diseases.
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9
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MUW researcher of the month. Wien Klin Wochenschr 2024; 136:126-127. [PMID: 38305880 DOI: 10.1007/s00508-024-02328-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
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10
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Patel AG, Ashenberg O, Collins NB, Segerstolpe Å, Jiang S, Slyper M, Huang X, Caraccio C, Jin H, Sheppard H, Xu K, Chang TC, Orr BA, Shirinifard A, Chapple RH, Shen A, Clay MR, Tatevossian RG, Reilly C, Patel J, Lupo M, Cline C, Dionne D, Porter CBM, Waldman J, Bai Y, Zhu B, Barrera I, Murray E, Vigneau S, Napolitano S, Wakiro I, Wu J, Grimaldi G, Dellostritto L, Helvie K, Rotem A, Lako A, Cullen N, Pfaff KL, Karlström Å, Jané-Valbuena J, Todres E, Thorner A, Geeleher P, Rodig SJ, Zhou X, Stewart E, Johnson BE, Wu G, Chen F, Yu J, Goltsev Y, Nolan GP, Rozenblatt-Rosen O, Regev A, Dyer MA. A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.574538. [PMID: 38260392 PMCID: PMC10802404 DOI: 10.1101/2024.01.07.574538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Neuroblastoma is a pediatric cancer arising from the developing sympathoadrenal lineage with complex inter- and intra-tumoral heterogeneity. To chart this complexity, we generated a comprehensive cell atlas of 55 neuroblastoma patient tumors, collected from two pediatric cancer institutions, spanning a range of clinical, genetic, and histologic features. Our atlas combines single-cell/nucleus RNA-seq (sc/scRNA-seq), bulk RNA-seq, whole exome sequencing, DNA methylation profiling, spatial transcriptomics, and two spatial proteomic methods. Sc/snRNA-seq revealed three malignant cell states with features of sympathoadrenal lineage development. All of the neuroblastomas had malignant cells that resembled sympathoblasts and the more differentiated adrenergic cells. A subset of tumors had malignant cells in a mesenchymal cell state with molecular features of Schwann cell precursors. DNA methylation profiles defined four groupings of patients, which differ in the degree of malignant cell heterogeneity and clinical outcomes. Using spatial proteomics, we found that neuroblastomas are spatially compartmentalized, with malignant tumor cells sequestered away from immune cells. Finally, we identify spatially restricted signaling patterns in immune cells from spatial transcriptomics. To facilitate the visualization and analysis of our atlas as a resource for further research in neuroblastoma, single cell, and spatial-omics, all data are shared through the Human Tumor Atlas Network Data Commons at www.humantumoratlas.org.
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Affiliation(s)
- Anand G Patel
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- These authors contributed equally
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally
| | - Natalie B Collins
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
- These authors contributed equally
| | - Åsa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xin Huang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chiara Caraccio
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather Sheppard
- Comparative Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ke Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Abbas Shirinifard
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard H Chapple
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Amber Shen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael R Clay
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ruth G Tatevossian
- Cancer Biomarkers Laboratory, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Colleen Reilly
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jaimin Patel
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Marybeth Lupo
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cynthia Cline
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Evan Murray
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sébastien Vigneau
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sara Napolitano
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Isaac Wakiro
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jingyi Wu
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Grace Grimaldi
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Laura Dellostritto
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Karla Helvie
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ana Lako
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicole Cullen
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kathleen L Pfaff
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Åsa Karlström
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ellen Todres
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aaron Thorner
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul Geeleher
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elizabeth Stewart
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bruce E Johnson
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Fei Chen
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yury Goltsev
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Current address: Research and Early Development, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Current address: Research and Early Development, Genentech Inc., South San Francisco, CA, 94080, USA
- Lead contacts
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Lead contacts
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11
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Guyer RA, Picard N, Mueller JL, Ohishi K, Leavitt A, Murphy AJ, Cornejo KM, Hotta R, Goldstein AM. Differentiated neuroblastoma cells remain epigenetically poised for de-differentiation to an immature state. Dis Model Mech 2023; 16:dmm049754. [PMID: 38095019 PMCID: PMC10810560 DOI: 10.1242/dmm.049754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/20/2023] [Indexed: 12/28/2023] Open
Abstract
Neuroblastoma is the most common extracranial solid tumor of childhood and accounts for a significant share of childhood cancer deaths. Prior studies utilizing RNA sequencing of bulk tumor populations showed two predominant cell states characterized by high and low expression of neuronal genes. Although cells respond to treatment by altering their gene expression, it is unclear whether this reflects shifting balances of distinct subpopulations or plasticity of individual cells. Using mouse and human neuroblastoma cell lines lacking MYCN amplification, we show that the antigen CD49b (also known as ITGA2) distinguishes these subpopulations. CD49b expression marked proliferative cells with an immature gene expression program, whereas CD49b-negative cells expressed differentiated neuronal marker genes and were non-cycling. Sorted populations spontaneously switched between CD49b expression states in culture, and CD49b-negative cells could generate rapidly growing, CD49b-positive tumors in mice. Although treatment with the chemotherapy drug doxorubicin selectively killed CD49b-positive cells in culture, the CD49b-positive population recovered when treatment was withdrawn. We profiled histone 3 (H3) lysine 27 acetylation (H3K27ac) to identify enhancers and super enhancers that were specifically active in each population and found that CD49b-negative cells maintained the priming H3 lysine 4 methylation (H3K4me1) mark at elements that were active in cells with high expression of CD49b. Improper maintenance of primed enhancer elements might thus underlie cellular plasticity in neuroblastoma, representing potential therapeutic targets for this lethal tumor.
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Affiliation(s)
- Richard A. Guyer
- Department of Pediatric Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicole Picard
- Department of Pediatric Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jessica L. Mueller
- Department of Pediatric Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kensuke Ohishi
- Department of Pediatric Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
- Drug Discovery Laboratory, Wakunaga Pharmaceutical Co. Ltd., Akitakata, Hiroshima 739-1195, Japan
| | - Abigail Leavitt
- Department of Pediatric Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Andrew J. Murphy
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38015, USA
| | - Kristine M. Cornejo
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ryo Hotta
- Department of Pediatric Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Allan M. Goldstein
- Department of Pediatric Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
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12
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Cheng MW, Mitra M, Coller HA. Pan-cancer landscape of epigenetic factor expression predicts tumor outcome. Commun Biol 2023; 6:1138. [PMID: 37973839 PMCID: PMC10654613 DOI: 10.1038/s42003-023-05459-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 10/13/2023] [Indexed: 11/19/2023] Open
Abstract
Oncogenic pathways that drive cancer progression reflect both genetic changes and epigenetic regulation. Here we stratified primary tumors from each of 24 TCGA adult cancer types based on the gene expression patterns of epigenetic factors (epifactors). The tumors for five cancer types (ACC, KIRC, LGG, LIHC, and LUAD) separated into two robust clusters that were better than grade or epithelial-to-mesenchymal transition in predicting clinical outcomes. The majority of epifactors that drove the clustering were also individually prognostic. A pan-cancer machine learning model deploying epifactor expression data for these five cancer types successfully separated the patients into poor and better outcome groups. Single-cell analysis of adult and pediatric tumors revealed that expression patterns associated with poor or worse outcomes were present in individual cells within tumors. Our study provides an epigenetic map of cancer types and lays a foundation for discovering pan-cancer targetable epifactors.
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Affiliation(s)
- Michael W Cheng
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Mithun Mitra
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Hilary A Coller
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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13
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Visser LL, Bleijs M, Margaritis T, van de Wetering M, Holstege FCP, Clevers H. Ewing Sarcoma Single-cell Transcriptome Analysis Reveals Functionally Impaired Antigen-presenting Cells. CANCER RESEARCH COMMUNICATIONS 2023; 3:2158-2169. [PMID: 37823774 PMCID: PMC10595530 DOI: 10.1158/2767-9764.crc-23-0027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/03/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023]
Abstract
Novel therapeutic strategies are urgently needed for patients with high-risk Ewing sarcoma and for the reduction of severe side effects for all patients. Immunotherapy may fill this need, but its successful application has been hampered by a lack of knowledge on the composition and function of the Ewing sarcoma immune microenvironment. Here, we explore the immune microenvironment of Ewing sarcoma, by single-cell RNA sequencing of 18 Ewing sarcoma primary tissue samples. Ewing sarcoma is infiltrated by natural killer, T, and B cells, dendritic cells, and immunosuppressive macrophages. Ewing sarcoma-associated T cells show various degrees of dysfunction. The antigen-presenting cells found in Ewing sarcoma lack costimulatory gene expression, implying functional impairment. Interaction analysis reveals a clear role for Ewing sarcoma tumor cells in turning the Ewing sarcoma immune microenvironment into an immunosuppressive niche. These results provide novel insights into the functional state of immune cells in the Ewing sarcoma tumor microenvironment and suggest mechanisms by which Ewing sarcoma tumor cells interact with, and shape, the immune microenvironment. SIGNIFICANCE This study is the first presenting a detailed analysis of the Ewing sarcoma microenvironment using single-cell RNA sequencing. We provide novel insight into the functional state of immune cells and suggests mechanisms by which Ewing tumor cells interact with, and shape, their immune microenvironment. These insights provide help in understanding the failures and successes of immunotherapy in Ewing sarcoma and may guide novel targeted (immuno) therapeutic approaches.
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Affiliation(s)
- Lindy L. Visser
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Margit Bleijs
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | | | - Frank C. P. Holstege
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Center for Molecular Medicine, UMC Utrecht and Utrecht University, Utrecht, the Netherlands
| | - Hans Clevers
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Centre, Utrecht, the Netherlands
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14
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D’Amico S, Tempora P, Gragera P, Król K, Melaiu O, De Ioris MA, Locatelli F, Fruci D. Two bullets in the gun: combining immunotherapy with chemotherapy to defeat neuroblastoma by targeting adrenergic-mesenchymal plasticity. Front Immunol 2023; 14:1268645. [PMID: 37849756 PMCID: PMC10577183 DOI: 10.3389/fimmu.2023.1268645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/18/2023] [Indexed: 10/19/2023] Open
Abstract
Neuroblastoma (NB) is a childhood tumor that originates in the peripheral sympathetic nervous system and is responsible for 15% of cancer-related deaths in the pediatric population. Despite intensive multimodal treatment, many patients with high-risk NB relapse and develop a therapy-resistant tumor. One of the phenomena related to therapeutic resistance is intratumor heterogeneity resulting from the adaptation of tumor cells in response to different selective environmental pressures. The transcriptional and epigenetic profiling of NB tissue has recently revealed the existence of two distinct cellular identities in the NB, termed adrenergic (ADRN) and mesenchymal (MES), which can spontaneously interconvert through epigenetic regulation. This phenomenon, known as tumor plasticity, has a major impact on cancer pathogenesis. The aim of this review is to describe the peculiarities of these two cell states, and how their plasticity affects the response to current therapeutic treatments, with special focus on the immunogenic potential of MES cells. Furthermore, we will discuss the opportunity to combine immunotherapy with chemotherapy to counteract NB phenotypic interconversion.
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Affiliation(s)
- Silvia D’Amico
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Patrizia Tempora
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Paula Gragera
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Kamila Król
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Ombretta Melaiu
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Clinical Sciences and Translational Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Maria Antonietta De Ioris
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Franco Locatelli
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Pediatrics, Catholic University of the Sacred Heart, Rome, Italy
| | - Doriana Fruci
- Department of Paediatric Haematology/Oncology and Cell and Gene Therapy, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
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15
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Agarwal P, Cadart C, Fort L, Gahan J, Greenspan L, Juan T, Kameneva P, Miao Y. Pathway to Independence: the future of developmental biology. Development 2023; 150:dev202360. [PMID: 37812057 DOI: 10.1242/dev.202360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
In 2022, Development launched its Pathway to Independence (PI) Programme, aimed at supporting postdocs as they transition to their first independent position. We selected eight talented researchers as the first cohort of PI Fellows. In this article, each of our Fellows provides their perspective on the future of their field. Together, they paint an exciting picture of the current state of and open questions in developmental biology.
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Affiliation(s)
- Priti Agarwal
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Clotilde Cadart
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Loic Fort
- Vanderbilt University School of Medicine, 465 21st Avenue South, U 3200 MRB III, Nashville, TN 37240-7935, USA
| | - James Gahan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Leah Greenspan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Thomas Juan
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, D-61231 Bad Nauheim, Germany
| | - Polina Kameneva
- The Medical University of Vienna, Spitalgasse 23, 1090 Vienna, Austria
| | - Yuchuan Miao
- Department of Genetics, Harvard Medical School and Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
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16
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Yuan Y, Alzrigat M, Rodriguez-Garcia A, Wang X, Bexelius TS, Johnsen JI, Arsenian-Henriksson M, Liaño-Pons J, Bedoya-Reina OC. Target Genes of c-MYC and MYCN with Prognostic Power in Neuroblastoma Exhibit Different Expressions during Sympathoadrenal Development. Cancers (Basel) 2023; 15:4599. [PMID: 37760568 PMCID: PMC10527308 DOI: 10.3390/cancers15184599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/06/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Deregulation of the MYC family of transcription factors c-MYC (encoded by MYC), MYCN, and MYCL is prevalent in most human cancers, with an impact on tumor initiation and progression, as well as response to therapy. In neuroblastoma (NB), amplification of the MYCN oncogene and over-expression of MYC characterize approximately 40% and 10% of all high-risk NB cases, respectively. However, the mechanism and stage of neural crest development in which MYCN and c-MYC contribute to the onset and/or progression of NB are not yet fully understood. Here, we hypothesized that subtle differences in the expression of MYCN and/or c-MYC targets could more accurately stratify NB patients in different risk groups rather than using the expression of either MYC gene alone. We employed an integrative approach using the transcriptome of 498 NB patients from the SEQC cohort and previously defined c-MYC and MYCN target genes to model a multigene transcriptional risk score. Our findings demonstrate that defined sets of c-MYC and MYCN targets with significant prognostic value, effectively stratify NB patients into different groups with varying overall survival probabilities. In particular, patients exhibiting a high-risk signature score present unfavorable clinical parameters, including increased clinical risk, higher INSS stage, MYCN amplification, and disease progression. Notably, target genes with prognostic value differ between c-MYC and MYCN, exhibiting distinct expression patterns in the developing sympathoadrenal system. Genes associated with poor outcomes are mainly found in sympathoblasts rather than in chromaffin cells during the sympathoadrenal development.
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Affiliation(s)
- Ye Yuan
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Mohammad Alzrigat
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Aida Rodriguez-Garcia
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Xueyao Wang
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Tomas Sjöberg Bexelius
- Paediatric Oncology Unit, Astrid Lindgren’s Children Hospital, SE-171 64 Solna, Sweden
- Department of Women’s and Children’s Health, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - John Inge Johnsen
- Department of Women’s and Children’s Health, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Judit Liaño-Pons
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Oscar C. Bedoya-Reina
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum, Karolinska Institutet, SE-171 65 Stockholm, Sweden
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17
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Wang X, Guo Y, Chen G, Fang E, Wang J, Li Q, Li D, Hu A, Bao B, Zhou Y, Gao H, Song J, Du X, Zheng L, Tong Q. Therapeutic targeting of FUBP3 phase separation by GATA2-AS1 inhibits malate-aspartate shuttle and neuroblastoma progression via modulating SUZ12 activity. Oncogene 2023; 42:2673-2687. [PMID: 37537343 DOI: 10.1038/s41388-023-02798-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023]
Abstract
Malate-aspartate shuttle (MAS) is essential for maintaining glycolysis and energy metabolism in tumors, while its regulatory mechanisms in neuroblastoma (NB), the commonest extracranial malignancy during childhood, still remain to be elucidated. Herein, by analyzing multi-omics data, GATA binding protein 2 (GATA2) and its antisense RNA 1 (GATA2-AS1) were identified to suppress MAS during NB progression. Mechanistic studies revealed that GATA2 inhibited the transcription of glutamic-oxaloacetic transaminase 2 (GOT2) and malate dehydrogenase 2 (MDH2). As a long non-coding RNA destabilized by RNA binding motif protein 15-mediated N6-methyladenosine methylation, GATA2-AS1 bound with far upstream element binding protein 3 (FUBP3) to repress its liquid-liquid phase separation and interaction with suppressor of zest 12 (SUZ12), resulting in decrease of SUZ12 activity and epigenetic up-regulation of GATA2 and other tumor suppressors. Rescue experiments revealed that GATA2-AS1 inhibited MAS and NB progression via repressing interaction between FUBP3 and SUZ12. Pre-clinically, administration of lentivirus carrying GATA2-AS1 suppressed MAS, aerobic glycolysis, and aggressive behaviors of NB xenografts. Notably, low GATA2-AS1 or GATA2 expression and high FUBP3, SUZ12, GOT2 or MDH2 levels were linked with unfavorable outcome of NB patients. These findings suggest that GATA2-AS1 inhibits FUBP3 phase separation to repress MAS and NB progression via modulating SUZ12 activity.
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Affiliation(s)
- Xiaojing Wang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China
| | - Yanhua Guo
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China
| | - Guo Chen
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China
| | - Erhu Fang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China
| | - Jianqun Wang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China
| | - Qilan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China
| | - Dan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China
| | - Anpei Hu
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China
| | - Banghe Bao
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China
| | - Yi Zhou
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China
| | - Haiyang Gao
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China
| | - Jiyu Song
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China
| | - Xinyi Du
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China
| | - Liduan Zheng
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China.
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China.
| | - Qiangsong Tong
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China.
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei Province, P. R. China.
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18
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del Valle I, Young MD, Kildisiute G, Ogunbiyi OK, Buonocore F, Simcock IC, Khabirova E, Crespo B, Moreno N, Brooks T, Niola P, Swarbrick K, Suntharalingham JP, McGlacken-Byrne SM, Arthurs OJ, Behjati S, Achermann JC. An integrated single-cell analysis of human adrenal cortex development. JCI Insight 2023; 8:e168177. [PMID: 37440461 PMCID: PMC10443814 DOI: 10.1172/jci.insight.168177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
The adrenal glands synthesize and release essential steroid hormones such as cortisol and aldosterone, but many aspects of human adrenal gland development are not well understood. Here, we combined single-cell and bulk RNA sequencing, spatial transcriptomics, IHC, and micro-focus computed tomography to investigate key aspects of adrenal development in the first 20 weeks of gestation. We demonstrate rapid adrenal growth and vascularization, with more cell division in the outer definitive zone (DZ). Steroidogenic pathways favored androgen synthesis in the central fetal zone, but DZ capacity to synthesize cortisol and aldosterone developed with time. Core transcriptional regulators were identified, with localized expression of HOPX (also known as Hop homeobox/homeobox-only protein) in the DZ. Potential ligand-receptor interactions between mesenchyme and adrenal cortex were seen (e.g., RSPO3/LGR4). Growth-promoting imprinted genes were enriched in the developing cortex (e.g., IGF2, PEG3). These findings reveal aspects of human adrenal development and have clinical implications for understanding primary adrenal insufficiency and related postnatal adrenal disorders, such as adrenal tumor development, steroid disorders, and neonatal stress.
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Affiliation(s)
- Ignacio del Valle
- Genetics and Genomic Medicine Research and Teaching Department, University College London (UCL) Great Ormond Street Institute of Child Health, UCL, London, United Kingdom
| | - Matthew D. Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Gerda Kildisiute
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Olumide K. Ogunbiyi
- Department of Histopathology, Great Ormond Street Hospital for Children National Health Service (NHS) Foundation Trust, London, United Kingdom
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, United Kingdom
| | - Federica Buonocore
- Genetics and Genomic Medicine Research and Teaching Department, University College London (UCL) Great Ormond Street Institute of Child Health, UCL, London, United Kingdom
| | - Ian C. Simcock
- Department of Clinical Radiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- National Institute of Health Research (NIHR) Great Ormond Street Biomedical Research Centre, London, United Kingdom
- Population, Policy and Practice Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, United Kingdom
| | - Eleonora Khabirova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Berta Crespo
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, United Kingdom
| | - Nadjeda Moreno
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, United Kingdom
| | - Tony Brooks
- UCL Genomics, Zayed Centre for Research, UCL Great Ormond Street Institute of Child Health, UCL, London, United Kingdom
| | - Paola Niola
- UCL Genomics, Zayed Centre for Research, UCL Great Ormond Street Institute of Child Health, UCL, London, United Kingdom
| | - Katherine Swarbrick
- Department of Histopathology, Great Ormond Street Hospital for Children National Health Service (NHS) Foundation Trust, London, United Kingdom
- Developmental Biology and Cancer Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, United Kingdom
| | - Jenifer P. Suntharalingham
- Genetics and Genomic Medicine Research and Teaching Department, University College London (UCL) Great Ormond Street Institute of Child Health, UCL, London, United Kingdom
| | - Sinead M. McGlacken-Byrne
- Genetics and Genomic Medicine Research and Teaching Department, University College London (UCL) Great Ormond Street Institute of Child Health, UCL, London, United Kingdom
| | - Owen J. Arthurs
- Department of Clinical Radiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- National Institute of Health Research (NIHR) Great Ormond Street Biomedical Research Centre, London, United Kingdom
- Population, Policy and Practice Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, UCL, London, United Kingdom
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - John C. Achermann
- Genetics and Genomic Medicine Research and Teaching Department, University College London (UCL) Great Ormond Street Institute of Child Health, UCL, London, United Kingdom
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19
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Anderson ND, Birch J, Accogli T, Criado I, Khabirova E, Parks C, Wood Y, Young MD, Porter T, Richardson R, Albon SJ, Popova B, Lopes A, Wynn R, Hough R, Gohil SH, Pule M, Amrolia PJ, Behjati S, Ghorashian S. Transcriptional signatures associated with persisting CD19 CAR-T cells in children with leukemia. Nat Med 2023; 29:1700-1709. [PMID: 37407840 PMCID: PMC10353931 DOI: 10.1038/s41591-023-02415-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/23/2023] [Indexed: 07/07/2023]
Abstract
In the context of relapsed and refractory childhood pre-B cell acute lymphoblastic leukemia (R/R B-ALL), CD19-targeting chimeric antigen receptor (CAR)-T cells often induce durable remissions, which requires the persistence of CAR-T cells. In this study, we systematically analyzed CD19 CAR-T cells of 10 children with R/R B-ALL enrolled in the CARPALL trial via high-throughput single-cell gene expression and T cell receptor sequencing of infusion products and serial blood and bone marrow samples up to 5 years after infusion. We show that long-lived CAR-T cells developed a CD4/CD8 double-negative phenotype with an exhausted-like memory state and distinct transcriptional signature. This persistence signature was dominant among circulating CAR-T cells in all children with a long-lived treatment response for which sequencing data were sufficient (4/4, 100%). The signature was also present across T cell subsets and clonotypes, indicating that persisting CAR-T cells converge transcriptionally. This persistence signature was also detected in two adult patients with chronic lymphocytic leukemia with decade-long remissions who received a different CD19 CAR-T cell product. Examination of single T cell transcriptomes from a wide range of healthy and diseased tissues across children and adults indicated that the persistence signature may be specific to long-lived CAR-T cells. These findings raise the possibility that a universal transcriptional signature of clinically effective, persistent CD19 CAR-T cells exists.
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Affiliation(s)
| | - Jack Birch
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Theo Accogli
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Ignacio Criado
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
| | | | | | | | | | | | - Rachel Richardson
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sarah J Albon
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Bilyana Popova
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Andre Lopes
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Robert Wynn
- Department of Bone Marrow Transplantation, Royal Manchester Children's Hospital, Manchester, UK
| | - Rachael Hough
- Children and Young People's Cancer Service, University College London Hospitals NHS Foundation Trust, London, UK
| | - Satyen H Gohil
- Department of Haematology, University College London Hospitals NHS Foundation Trust, London, UK
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Martin Pule
- Department of Haematology, UCL Cancer Institute, London, UK
| | - Persis J Amrolia
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, UK
- Department of Bone Marrow Transplantation, Great Ormond Street Hospital for Children, London, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
| | - Sara Ghorashian
- Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK.
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK.
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20
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Fanlo L, Gómez-González S, Rozalén C, Pérez-Núñez I, Sangrador I, Tomás-Daza L, Gautier EL, Usieto S, Rebollo E, Vila-Ubach M, Carcaboso AM, Javierre BM, Celià-Terrassa T, Lavarino C, Martí E, Le Dréau G. Neural crest-related NXPH1/α-NRXN signaling opposes neuroblastoma malignancy by inhibiting organotropic metastasis. Oncogene 2023:10.1038/s41388-023-02742-2. [PMID: 37301928 DOI: 10.1038/s41388-023-02742-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/16/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Neuroblastoma is a pediatric cancer that can present as low- or high-risk tumors (LR-NBs and HR-NBs), the latter group showing poor prognosis due to metastasis and strong resistance to current therapy. Whether LR-NBs and HR-NBs differ in the way they exploit the transcriptional program underlying their neural crest, sympatho-adrenal origin remains unclear. Here, we identified the transcriptional signature distinguishing LR-NBs from HR-NBs, which consists mainly of genes that belong to the core sympatho-adrenal developmental program and are associated with favorable patient prognosis and with diminished disease progression. Gain- and loss-of-function experiments revealed that the top candidate gene of this signature, Neurexophilin-1 (NXPH1), has a dual impact on NB cell behavior in vivo: whereas NXPH1 and its receptor α-NRXN1 promote NB tumor growth by stimulating cell proliferation, they conversely inhibit organotropic colonization and metastasis. As suggested by RNA-seq analyses, these effects might result from the ability of NXPH1/α-NRXN signalling to restrain the conversion of NB cells from an adrenergic state to a mesenchymal one. Our findings thus uncover a transcriptional module of the sympatho-adrenal program that opposes neuroblastoma malignancy by impeding metastasis, and pinpoint NXPH1/α-NRXN signaling as a promising target to treat HR-NBs.
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Affiliation(s)
- Lucía Fanlo
- Department of Cells and Tissues, Instituto de Biología Molecular de Barcelona, CSIC, Parc Científic de Barcelona, C/ Baldiri Reixac 10-15, 08028, Barcelona, Spain
| | - Soledad Gómez-González
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - Catalina Rozalén
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003, Barcelona, Spain
| | - Iván Pérez-Núñez
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003, Barcelona, Spain
| | - Irene Sangrador
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003, Barcelona, Spain
| | | | - Emmanuel L Gautier
- Institut National de la Santé et de la Recherche Médicale (Inserm, UMR_S 1166), Sorbonne Université, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Susana Usieto
- Department of Cells and Tissues, Instituto de Biología Molecular de Barcelona, CSIC, Parc Científic de Barcelona, C/ Baldiri Reixac 10-15, 08028, Barcelona, Spain
| | - Elena Rebollo
- Molecular Imaging Platform, Instituto de Biología Molecular de Barcelona, CSIC, Parc Científic de Barcelona, C/ Baldiri Reixac 10-15, 08028, Barcelona, Spain
| | - Mònica Vila-Ubach
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - Angel M Carcaboso
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - Biola M Javierre
- Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Spain
| | - Toni Celià-Terrassa
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003, Barcelona, Spain
| | - Cinzia Lavarino
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - Elisa Martí
- Department of Cells and Tissues, Instituto de Biología Molecular de Barcelona, CSIC, Parc Científic de Barcelona, C/ Baldiri Reixac 10-15, 08028, Barcelona, Spain
| | - Gwenvael Le Dréau
- Department of Cells and Tissues, Instituto de Biología Molecular de Barcelona, CSIC, Parc Científic de Barcelona, C/ Baldiri Reixac 10-15, 08028, Barcelona, Spain.
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012, Paris, France.
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21
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Huang H, Wu L, Lu L, Zhang Z, Qiu B, Mo J, Luo Y, Xi Z, Feng M, Wan P, Zhu J, Yu D, Wu W, Tan K, Liu J, Sheng Q, Xu T, Huang J, Lv Z, Tang Y, Xia Q. Single-cell transcriptomics uncovers cellular architecture and developmental trajectories in hepatoblastoma. Hepatology 2023; 77:1911-1928. [PMID: 36059151 DOI: 10.1002/hep.32775] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 08/19/2022] [Accepted: 08/30/2022] [Indexed: 12/08/2022]
Abstract
BACKGROUND AND AIMS Hepatoblastoma (HB) is the predominant type of childhood liver cancer. Treatment options for the clinically advanced HB remain limited. We aimed to dissect the cellular and molecular basis underlying HB oncogenesis and heterogeneity at the single-cell level, which could facilitate a better understanding of HB at both the biological and clinical levels. APPROACH AND RESULTS Single-cell transcriptome profiling of tumor and paired distal liver tissue samples from five patients with HB was performed. Deconvolution analysis was used for integrating the single-cell transcriptomic profiles with the bulk transcriptomes of our HB cohort of post-neoadjuvant chemotherapy tumor samples. A single-cell transcriptomic landscape of early human liver parenchymal development was established for exploring the cellular root and hierarchy of HB oncogenesis. As a result, seven distinct tumor cell subpopulations were annotated, and an effective HB subtyping method was established based on their compositions. A HB tumor cell hierarchy was further revealed to not only fit with the classical cancer stem cell (CSC) model but also mirror the early human liver parenchymal development. Moreover, FACT inhibition, which could disrupt the oncogenic positive feedback loop between MYC and SSRP1 in HB, was identified as a promising epigenetic-targeted therapeutic strategy against the CSC-like HB1-Pro-like1 subpopulation and its related high-risk "Pro-like1" subtype of HB. CONCLUSIONS Our findings illustrate the cellular architecture and developmental trajectories of HB via integrative bulk and single-cell transcriptome analyses, thus establishing a resourceful framework for the development of targeted diagnostics and therapeutics in the future.
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Affiliation(s)
- Hongting Huang
- Department of Liver Surgery, Renji Hospital, School of Medicine , Shanghai Jiaotong University , Shanghai , China
| | - Liang Wu
- Research Center of Translational Medicine, Shanghai Children's Hospital, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology , Shanghai Jiaotong University School of Medicine , Shanghai , China
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, School of Medicine , Shanghai Jiaotong University , Shanghai , China
| | - Li Lu
- Research Center of Translational Medicine, Shanghai Children's Hospital, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology , Shanghai Jiaotong University School of Medicine , Shanghai , China
- Department of General Surgery, Shanghai Children's Hospital , Shanghai Jiaotong University , Shanghai , China
| | - Zijie Zhang
- Department of Liver Surgery, Renji Hospital, School of Medicine , Shanghai Jiaotong University , Shanghai , China
| | - Bijun Qiu
- Department of Liver Surgery, Renji Hospital, School of Medicine , Shanghai Jiaotong University , Shanghai , China
| | - Jialin Mo
- Research Center of Translational Medicine, Shanghai Children's Hospital, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology , Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Yi Luo
- Department of Liver Surgery, Renji Hospital, School of Medicine , Shanghai Jiaotong University , Shanghai , China
| | - Zhifeng Xi
- Department of Liver Surgery, Renji Hospital, School of Medicine , Shanghai Jiaotong University , Shanghai , China
| | - Mingxuan Feng
- Department of Liver Surgery, Renji Hospital, School of Medicine , Shanghai Jiaotong University , Shanghai , China
| | - Ping Wan
- Department of Liver Surgery, Renji Hospital, School of Medicine , Shanghai Jiaotong University , Shanghai , China
| | - Jianjun Zhu
- Department of Liver Surgery, Renji Hospital, School of Medicine , Shanghai Jiaotong University , Shanghai , China
| | - Dingye Yu
- Department of Gastrointestinal Surgery , Renji Hospital, Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Wei Wu
- Department of General Surgery, Shanghai Children's Hospital , Shanghai Jiaotong University , Shanghai , China
| | - Kezhe Tan
- Department of General Surgery, Shanghai Children's Hospital , Shanghai Jiaotong University , Shanghai , China
| | - Jiangbin Liu
- Department of General Surgery, Shanghai Children's Hospital , Shanghai Jiaotong University , Shanghai , China
| | - Qingfeng Sheng
- Department of General Surgery, Shanghai Children's Hospital , Shanghai Jiaotong University , Shanghai , China
| | - Ting Xu
- Department of General Surgery, Shanghai Children's Hospital , Shanghai Jiaotong University , Shanghai , China
| | - Jinyan Huang
- Biomedical Big Data Center , The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou , China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease , Zhejiang University School of Medicine First Affiliated Hospital , Hangzhou , China
- Zhejiang University Cancer Center , Zhejiang University , Hangzhou , China
| | - Zhibao Lv
- Department of General Surgery, Shanghai Children's Hospital , Shanghai Jiaotong University , Shanghai , China
| | - Yujie Tang
- Research Center of Translational Medicine, Shanghai Children's Hospital, Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, Department of Pathophysiology , Shanghai Jiaotong University School of Medicine , Shanghai , China
- Shanghai Key Laboratory of Reproductive Medicine, Department of Histoembryology, Genetics and Developmental Biology , Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, School of Medicine , Shanghai Jiaotong University , Shanghai , China
- Shanghai Engineering Research Centre of Transplantation and Immunology , Shanghai , China
- Shanghai Institute of Transplantation , Shanghai , China
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22
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Zage PE, Huo Y, Subramonian D, Le Clorennec C, Ghosh P, Sahoo D. Identification of a novel gene signature for neuroblastoma differentiation using a Boolean implication network. Genes Chromosomes Cancer 2023; 62:313-331. [PMID: 36680522 PMCID: PMC10257350 DOI: 10.1002/gcc.23124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
Although induction of differentiation represents an effective strategy for neuroblastoma treatment, the mechanisms underlying neuroblastoma differentiation are poorly understood. We generated a computational model of neuroblastoma differentiation consisting of interconnected gene clusters identified based on symmetric and asymmetric gene expression relationships. We identified a differentiation signature consisting of series of gene clusters comprised of 1251 independent genes that predicted neuroblastoma differentiation in independent datasets and in neuroblastoma cell lines treated with agents known to induce differentiation. This differentiation signature was associated with patient outcomes in multiple independent patient cohorts and validated the role of MYCN expression as a marker of neuroblastoma differentiation. Our results further identified novel genes associated with MYCN via asymmetric Boolean implication relationships that would not have been identified using symmetric computational approaches and that were associated with both neuroblastoma differentiation and patient outcomes. Our differentiation signature included a cluster of genes involved in intracellular signaling and growth factor receptor trafficking pathways that is strongly associated with neuroblastoma differentiation, and we validated the associations of UBE4B, a gene within this cluster, with neuroblastoma cell and tumor differentiation. Our findings demonstrate that Boolean network analyses of symmetric and asymmetric gene expression relationships can identify novel genes and pathways relevant for neuroblastoma tumor differentiation that could represent potential therapeutic targets.
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Affiliation(s)
- Peter E. Zage
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego (UCSD), La Jolla, CA
| | - Yuchen Huo
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego (UCSD), La Jolla, CA
| | - Divya Subramonian
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego (UCSD), La Jolla, CA
| | - Christophe Le Clorennec
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego (UCSD), La Jolla, CA
| | - Pradipta Ghosh
- Department of Medicine, UCSD, La Jolla, CA
- Department of Cellular and Molecular Medicine, UCSD, La Jolla, CA
- Veterans Affairs Medical Center, La Jolla, CA
| | - Debashis Sahoo
- Department of Pediatrics, Division of Hematology-Oncology, University of California San Diego (UCSD), La Jolla, CA
- Department of Computer Science and Engineering, Jacobs School of Engineering, UCSD, La Jolla, CA
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23
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Hagemann S, Misiak D, Bell JL, Fuchs T, Lederer MI, Bley N, Hämmerle M, Ghazy E, Sippl W, Schulte JH, Hüttelmaier S. IGF2BP1 induces neuroblastoma via a druggable feedforward loop with MYCN promoting 17q oncogene expression. Mol Cancer 2023; 22:88. [PMID: 37246217 DOI: 10.1186/s12943-023-01792-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/19/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Neuroblastoma is the most common solid tumor in infants accounting for approximately 15% of all cancer-related deaths. Over 50% of high-risk neuroblastoma relapse, emphasizing the need of novel drug targets and therapeutic strategies. In neuroblastoma, chromosomal gains at chromosome 17q, including IGF2BP1, and MYCN amplification at chromosome 2p are associated with adverse outcome. Recent, pre-clinical evidence indicates the feasibility of direct and indirect targeting of IGF2BP1 and MYCN in cancer treatment. METHODS Candidate oncogenes on 17q were identified by profiling the transcriptomic/genomic landscape of 100 human neuroblastoma samples and public gene essentiality data. Molecular mechanisms and gene expression profiles underlying the oncogenic and therapeutic target potential of the 17q oncogene IGF2BP1 and its cross-talk with MYCN were characterized and validated in human neuroblastoma cells, xenografts and PDX as well as novel IGF2BP1/MYCN transgene mouse models. RESULTS We reveal a novel, druggable feedforward loop of IGF2BP1 (17q) and MYCN (2p) in high-risk neuroblastoma. This promotes 2p/17q chromosomal gains and unleashes an oncogene storm resulting in fostered expression of 17q oncogenes like BIRC5 (survivin). Conditional, sympatho-adrenal transgene expression of IGF2BP1 induces neuroblastoma at a 100% incidence. IGF2BP1-driven malignancies are reminiscent to human high-risk neuroblastoma, including 2p/17q-syntenic chromosomal gains and upregulation of Mycn, Birc5, as well as key neuroblastoma circuit factors like Phox2b. Co-expression of IGF2BP1/MYCN reduces disease latency and survival probability by fostering oncogene expression. Combined inhibition of IGF2BP1 by BTYNB, MYCN by BRD inhibitors or BIRC5 by YM-155 is beneficial in vitro and, for BTYNB, also. CONCLUSION We reveal a novel, druggable neuroblastoma oncogene circuit settling on strong, transcriptional/post-transcriptional synergy of MYCN and IGF2BP1. MYCN/IGF2BP1 feedforward regulation promotes an oncogene storm harboring high therapeutic potential for combined, targeted inhibition of IGF2BP1, MYCN expression and MYCN/IGF2BP1-effectors like BIRC5.
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Affiliation(s)
- Sven Hagemann
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany.
| | - Danny Misiak
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Jessica L Bell
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Tommy Fuchs
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Marcell I Lederer
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Nadine Bley
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Monika Hämmerle
- Institute of Pathology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Ehab Ghazy
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Johannes H Schulte
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany.
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24
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Thirant C, Peltier A, Durand S, Kramdi A, Louis-Brennetot C, Pierre-Eugène C, Gautier M, Costa A, Grelier A, Zaïdi S, Gruel N, Jimenez I, Lapouble E, Pierron G, Sitbon D, Brisse HJ, Gauthier A, Fréneaux P, Grossetête S, Baudrin LG, Raynal V, Baulande S, Bellini A, Bhalshankar J, Carcaboso AM, Geoerger B, Rohrer H, Surdez D, Boeva V, Schleiermacher G, Delattre O, Janoueix-Lerosey I. Reversible transitions between noradrenergic and mesenchymal tumor identities define cell plasticity in neuroblastoma. Nat Commun 2023; 14:2575. [PMID: 37142597 PMCID: PMC10160107 DOI: 10.1038/s41467-023-38239-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/21/2023] [Indexed: 05/06/2023] Open
Abstract
Noradrenergic and mesenchymal identities have been characterized in neuroblastoma cell lines according to their epigenetic landscapes and core regulatory circuitries. However, their relationship and relative contribution in patient tumors remain poorly defined. We now document spontaneous and reversible plasticity between the two identities, associated with epigenetic reprogramming, in several neuroblastoma models. Interestingly, xenografts with cells from each identity eventually harbor a noradrenergic phenotype suggesting that the microenvironment provides a powerful pressure towards this phenotype. Accordingly, such a noradrenergic cell identity is systematically observed in single-cell RNA-seq of 18 tumor biopsies and 15 PDX models. Yet, a subpopulation of these noradrenergic tumor cells presents with mesenchymal features that are shared with plasticity models, indicating that the plasticity described in these models has relevance in neuroblastoma patients. This work therefore emphasizes that intrinsic plasticity properties of neuroblastoma cells are dependent upon external cues of the environment to drive cell identity.
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Affiliation(s)
- Cécile Thirant
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Agathe Peltier
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Simon Durand
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Amira Kramdi
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Caroline Louis-Brennetot
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Cécile Pierre-Eugène
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Margot Gautier
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Ana Costa
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Amandine Grelier
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Sakina Zaïdi
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Nadège Gruel
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- Institut Curie, Department of Translational Research, Paris, France
| | - Irène Jimenez
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
- Institut Curie, Department of Translational Research, Paris, France
- Institut Curie, Laboratoire Recherche Translationnelle en Oncologie Pédiatrique (RTOP), Laboratoire "Gilles Thomas", Paris, France
| | - Eve Lapouble
- Institut Curie, Unité de Génétique Somatique, Paris, France
| | - Gaëlle Pierron
- Institut Curie, Unité de Génétique Somatique, Paris, France
| | - Déborah Sitbon
- Institut Curie, Unité de Génétique Somatique, Paris, France
| | - Hervé J Brisse
- Institut Curie, Department of Imaging, PSL Research University, Paris, France
| | | | - Paul Fréneaux
- Institut Curie, Department of Biopathology, Paris, France
| | - Sandrine Grossetête
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Laura G Baudrin
- Institut Curie, Genomics of Excellence (ICGex) Platform, Paris, France. Institut Curie, Single Cell Initiative, Paris, France
| | - Virginie Raynal
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- Institut Curie, Genomics of Excellence (ICGex) Platform, Paris, France. Institut Curie, Single Cell Initiative, Paris, France
| | - Sylvain Baulande
- Institut Curie, Genomics of Excellence (ICGex) Platform, Paris, France. Institut Curie, Single Cell Initiative, Paris, France
| | - Angela Bellini
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
- Institut Curie, Department of Translational Research, Paris, France
- Institut Curie, Laboratoire Recherche Translationnelle en Oncologie Pédiatrique (RTOP), Laboratoire "Gilles Thomas", Paris, France
| | - Jaydutt Bhalshankar
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
- Institut Curie, Department of Translational Research, Paris, France
- Institut Curie, Laboratoire Recherche Translationnelle en Oncologie Pédiatrique (RTOP), Laboratoire "Gilles Thomas", Paris, France
| | - Angel M Carcaboso
- SJD Pediatric Cancer Center Barcelona, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Birgit Geoerger
- Gustave Roussy Cancer Campus, INSERM U1015, Department of Pediatric and Adolescent Oncology, Université Paris-Saclay, Villejuif, France
| | - Hermann Rohrer
- Institute of Clinical Neuroanatomy, Dr. Senckenberg Anatomy, Neuroscience Center, Goethe University, Frankfurt/M, Germany
| | - Didier Surdez
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
- Balgrist University Hospital, Faculty of Medicine, University of Zurich (UZH), Zurich, Switzerland
| | - Valentina Boeva
- Inserm, U1016, Cochin Institute, CNRS UMR8104, Paris University, Paris, France
- ETH Zürich, Department of Computer Science, Institute for Machine Learning, Zürich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Zürich, Switzerland
| | - Gudrun Schleiermacher
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
- Institut Curie, Department of Translational Research, Paris, France
- Institut Curie, Laboratoire Recherche Translationnelle en Oncologie Pédiatrique (RTOP), Laboratoire "Gilles Thomas", Paris, France
| | - Olivier Delattre
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
- Institut Curie, Unité de Génétique Somatique, Paris, France
| | - Isabelle Janoueix-Lerosey
- Institut Curie, Inserm U830, PSL Research University, Diversity and Plasticity of Childhood Tumors Lab, Paris, France.
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.
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25
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Zunitch MJ, Fisch AS, Lin B, Barrios-Camacho CM, Faquin WC, Tachie-Baffour Y, Louie JD, Jang W, Curry WT, Gray ST, Lin DT, Schwob JE, Holbrook EH. Molecular Evidence for Olfactory Neuroblastoma as a Tumor of Malignant Globose Basal Cells. Mod Pathol 2023; 36:100122. [PMID: 36841178 PMCID: PMC10198888 DOI: 10.1016/j.modpat.2023.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/20/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023]
Abstract
Olfactory neuroblastoma (ONB, esthesioneuroblastoma) is a sinonasal cancer with an underdeveloped diagnostic toolkit, and is the subject of many incidents of tumor misclassification throughout the literature. Despite its name, connections between the cancer and normal cells of the olfactory epithelium have not been systematically explored and markers of olfactory epithelial cell types are not deployed in clinical practice. Here, we utilize an integrated human-mouse single-cell atlas of the nasal mucosa, including the olfactory epithelium, to identify transcriptomic programs that link ONB to a specific population of stem/progenitor cells known as olfactory epithelial globose basal cells (GBCs). Expression of a GBC transcription factor NEUROD1 distinguishes both low- and high-grade ONB from sinonasal undifferentiated carcinoma, a potential histologic mimic with a distinctly unfavorable prognosis. Furthermore, we identify a reproducible subpopulation of highly proliferative ONB cells expressing the GBC stemness marker EZH2, suggesting that EZH2 inhibition may play a role in the targeted treatment of ONB. Finally, we study the cellular states comprising ONB parenchyma using single-cell transcriptomics and identify evidence of a conserved GBC transcriptional regulatory circuit that governs divergent neuronal-versus-sustentacular differentiation. These results link ONB to a specific cell type for the first time and identify conserved developmental pathways within ONB that inform diagnostic, prognostic, and mechanistic investigation.
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Affiliation(s)
- Matthew J Zunitch
- Medical Scientist Training Program, Tufts University School of Medicine, Boston, Massachusetts; Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts
| | - Adam S Fisch
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Brian Lin
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - William C Faquin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yaw Tachie-Baffour
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts
| | - Jonathan D Louie
- Medical Scientist Training Program, Tufts University School of Medicine, Boston, Massachusetts; Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts
| | - Woochan Jang
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts
| | - William T Curry
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stacey T Gray
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts
| | - Derrick T Lin
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts
| | - James E Schwob
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts; Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts.
| | - Eric H Holbrook
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts.
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26
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Körber V, Stainczyk SA, Kurilov R, Henrich KO, Hero B, Brors B, Westermann F, Höfer T. Neuroblastoma arises in early fetal development and its evolutionary duration predicts outcome. Nat Genet 2023; 55:619-630. [PMID: 36973454 PMCID: PMC10101850 DOI: 10.1038/s41588-023-01332-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 02/06/2023] [Indexed: 03/29/2023]
Abstract
AbstractNeuroblastoma, the most frequent solid tumor in infants, shows very diverse outcomes from spontaneous regression to fatal disease. When these different tumors originate and how they evolve are not known. Here we quantify the somatic evolution of neuroblastoma by deep whole-genome sequencing, molecular clock analysis and population-genetic modeling in a comprehensive cohort covering all subtypes. We find that tumors across the entire clinical spectrum begin to develop via aberrant mitoses as early as the first trimester of pregnancy. Neuroblastomas with favorable prognosis expand clonally after short evolution, whereas aggressive neuroblastomas show prolonged evolution during which they acquire telomere maintenance mechanisms. The initial aneuploidization events condition subsequent evolution, with aggressive neuroblastoma exhibiting early genomic instability. We find in the discovery cohort (n = 100), and validate in an independent cohort (n = 86), that the duration of evolution is an accurate predictor of outcome. Thus, insight into neuroblastoma evolution may prospectively guide treatment decisions.
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27
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Zhao Z, Feng Q, Zhang Y, Ning Z. Adaptive risk-aware sharable and individual subspace learning for cancer survival analysis with multi-modality data. Brief Bioinform 2023; 24:6847200. [PMID: 36433784 DOI: 10.1093/bib/bbac489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/16/2022] [Accepted: 10/15/2022] [Indexed: 11/27/2022] Open
Abstract
Biomedical multi-modality data (also named multi-omics data) refer to data that span different types and derive from multiple sources in clinical practices (e.g. gene sequences, proteomics and histopathological images), which can provide comprehensive perspectives for cancers and generally improve the performance of survival models. However, the performance improvement of multi-modality survival models may be hindered by two key issues as follows: (1) how to learn and fuse modality-sharable and modality-individual representations from multi-modality data; (2) how to explore the potential risk-aware characteristics in each risk subgroup, which is beneficial to risk stratification and prognosis evaluation. Additionally, learning-based survival models generally refer to numerous hyper-parameters, which requires time-consuming parameter setting and might result in a suboptimal solution. In this paper, we propose an adaptive risk-aware sharable and individual subspace learning method for cancer survival analysis. The proposed method jointly learns sharable and individual subspaces from multi-modality data, whereas two auxiliary terms (i.e. intra-modality complementarity and inter-modality incoherence) are developed to preserve the complementary and distinctive properties of each modality. Moreover, it equips with a grouping co-expression constraint for obtaining risk-aware representation and preserving local consistency. Furthermore, an adaptive-weighted strategy is employed to efficiently estimate crucial parameters during the training stage. Experimental results on three public datasets demonstrate the superiority of our proposed model.
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Affiliation(s)
- Zhangxin Zhao
- School of Biomedical Engineering at Southern Medical University, Guangdong, China
| | - Qianjin Feng
- School of Biomedical Engineering at Southern Medical University, Guangdong, China
| | - Yu Zhang
- School of Biomedical Engineering, Southern Medical University, Guangdong, China
| | - Zhenyuan Ning
- School of Biomedical Engineering at Southern Medical University, Guangdong, China
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28
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Chen ZF, Wu LZ, Chen ZT, Su LJ, Fu CJ. The potential mechanisms of neuroblastoma in children based on bioinformatics big data. Transl Pediatr 2022; 11:1908-1919. [PMID: 36643678 PMCID: PMC9834953 DOI: 10.21037/tp-22-504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In recent years, miRNAs have become a research hotspot, which is related to the occurrence and development of a variety of malignant tumors, but there are few studies in neuroblastoma. In this study, the differentially expressed microRNAs (miRNAs) in neuroblastoma were identified and analyzed using bioinformatics, and their biological functions and related signaling pathways were examined. METHODS The neuroblastoma miRNA chip GSE121513 was obtained from the Gene Expression Omnibus (GEO) database and the data of 95 neuroblastoma samples and normal fetal adrenal neuroblastoma samples were analyzed to screen the differential miRNAs. The target genes of the differentially expressed miRNAs were predicted using |log fold change (FC)| ≥4. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were performed to construct a protein-protein interaction network and identify the core target genes. RESULTS A total of 91 differentially expressed miRNAs were identified (P<0.05, |logFC| ≥1), including 52 upregulated and 39 downregulated miRNAs. The target genes of the differential miRNAs (P<0.05, |logFC| ≥4) were pretested, and 602 target genes were obtained. Functional analysis showed that these genes were mainly located in the extracellular matrix region of proteins, and were involved in the negative regulation of cytoplasmic translation, mRNA 3'-untranslated region (UTR) binding, and binding to nucleic acid to inhibit the activity of translation factors. They were also involved in RNA degradation, adhesion pathways, and the phosphatidylinositol-3-kinase (PI3K)-Akt signaling pathway. Ten key target genes were identified via protein interaction network screening. CONCLUSIONS The differential miRNAs may be related to the occurrence of neuroblastoma were screened.
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Affiliation(s)
- Ze-Fu Chen
- Department of Pediatrics, Hainan General Hospital, Haikou, China
| | - Li-Zhen Wu
- Department of Operating Theater, Hainan General Hospital, Haikou, China
| | - Ze-Ting Chen
- Department of Pediatric Surgery, Hainan General Hospital, Haikou, China
| | - Liang-Ju Su
- Department of Pediatric Surgery, Hainan General Hospital, Haikou, China
| | - Ce-Jun Fu
- Department of Pediatric Surgery, Hainan General Hospital, Haikou, China
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29
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Neves JB, Roberts K, Nguyen JS, El Sheikh S, Tran-Dang MA, Horsfield C, Mumtaz F, Campbell P, Stauss H, Tran MG, Mitchell T. Defining the origin, evolution, and immune composition of SDH-deficient renal cell carcinoma. iScience 2022; 25:105389. [PMID: 36345344 PMCID: PMC9636038 DOI: 10.1016/j.isci.2022.105389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/05/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Succinate dehydrogenase (SDH)-deficient renal cell carcinoma represents a rare subtype of hereditary kidney cancer. Clinical diagnosis can be challenging and there is little evidence to guide systemic therapeutic options. We performed genomic profiling of a cohort of tumors through the analysis of whole genomes, transcriptomes, as well as flow cytometry and immunohistochemistry in order to gain a deeper understanding of their molecular biology. We find neutral evolution after early tumor activation with a lack of secondary driver events. We show that these tumors have epithelial derivation, possibly from the macula densa, a specialized paracrine cell of the renal juxtaglomerular apparatus. They subsequently develop into immune excluded tumors. We provide transcriptomic and protein expression evidence of a highly specific tumor marker, PAPPA2. These translational findings have implications for the diagnosis and treatment for this rare tumor subtype.
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Affiliation(s)
- Joana B. Neves
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London, UK
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London, UK
- UCL Institute of Immunity & Transplantation, The Pears Building, Pond Street, London, UK
| | - Kirsty Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Soha El Sheikh
- Department of Histopathology, Royal Free Hospital, London, UK
| | | | - Catherine Horsfield
- Guy’s & St Thomas’ National Health Service Trust, Westminster Bridge Road, London, UK
| | - Faiz Mumtaz
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London, UK
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London, UK
| | - Peter Campbell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Hans Stauss
- UCL Institute of Immunity & Transplantation, The Pears Building, Pond Street, London, UK
| | - Maxine G.B. Tran
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London, UK
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London, UK
- UCL Institute of Immunity & Transplantation, The Pears Building, Pond Street, London, UK
| | - Thomas Mitchell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
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30
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Mañas A, Aaltonen K, Andersson N, Hansson K, Adamska A, Seger A, Yasui H, van den Bos H, Radke K, Esfandyari J, Bhave MS, Karlsson J, Spierings D, Foijer F, Gisselsson D, Bexell D. Clinically relevant treatment of PDX models reveals patterns of neuroblastoma chemoresistance. SCIENCE ADVANCES 2022; 8:eabq4617. [PMID: 36306349 PMCID: PMC9616506 DOI: 10.1126/sciadv.abq4617] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Chemotherapy resistance and relapses are common in high-risk neuroblastoma (NB). Here, we developed a clinically relevant in vivo treatment protocol mimicking the first-line five-chemotherapy treatment regimen of high-risk NB and applied this protocol to mice with MYCN-amplified NB patient-derived xenografts (PDXs). Genomic and transcriptomic analyses were used to reveal NB chemoresistance mechanisms. Intrinsic resistance was associated with high genetic diversity and an embryonic phenotype. Relapsed NB with acquired resistance showed a decreased adrenergic phenotype and an enhanced immature mesenchymal-like phenotype, resembling multipotent Schwann cell precursors. NBs with a favorable treatment response presented a lineage-committed adrenergic phenotype similar to normal neuroblasts. Novel integrated phenotypic gene signatures reflected treatment response and patient prognosis. NB organoids established from relapsed PDX tumors retained drug resistance, tumorigenicity, and transcriptional cell states. This work sheds light on the mechanisms of NB chemotherapy response and emphasizes the importance of transcriptional cell states in chemoresistance.
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Affiliation(s)
- Adriana Mañas
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Kristina Aaltonen
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Natalie Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund 22185, Sweden
| | - Karin Hansson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
- Cancer Stem Cell Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Aleksandra Adamska
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Alexandra Seger
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Hiroaki Yasui
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund 22185, Sweden
- Department of Gynecologic Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, AV, Groningen 9713, Netherlands
| | - Katarzyna Radke
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Javanshir Esfandyari
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Madhura Satish Bhave
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
| | - Jenny Karlsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund 22185, Sweden
| | - Diana Spierings
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, AV, Groningen 9713, Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, AV, Groningen 9713, Netherlands
| | - David Gisselsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund 22185, Sweden
- Department of Pathology, Laboratory Medicine, Skane University Hospital, Lund 22184, Sweden
| | - Daniel Bexell
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, Lund 22381, Sweden
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31
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Single-cell profiling of peripheral neuroblastic tumors identifies an aggressive transitional state that bridges an adrenergic-mesenchymal trajectory. Cell Rep 2022; 41:111455. [DOI: 10.1016/j.celrep.2022.111455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 04/16/2022] [Accepted: 09/14/2022] [Indexed: 11/21/2022] Open
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32
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Gomez RL, Ibragimova S, Ramachandran R, Philpott A, Ali FR. Tumoral heterogeneity in neuroblastoma. Biochim Biophys Acta Rev Cancer 2022; 1877:188805. [PMID: 36162542 DOI: 10.1016/j.bbcan.2022.188805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/28/2022] [Accepted: 09/17/2022] [Indexed: 10/31/2022]
Abstract
Neuroblastoma is a solid, neuroendocrine tumor with divergent clinical behavior ranging from asymptomatic to fatal. The diverse clinical presentations of neuroblastoma are directly linked to the high intra- and inter-tumoral heterogeneity it presents. This heterogeneity is strongly associated with therapeutic resistance and continuous relapses, often leading to fatal outcomes. The development of successful risk assessment and tailored treatment strategies lies in evaluating the extent of heterogeneity via the accurate genetic and epigenetic profiling of distinct cell subpopulations present in the tumor. Recent studies have focused on understanding the molecular mechanisms that drive tumoral heterogeneity in pursuing better therapeutic and diagnostic approaches. This review describes the cellular, genetic, and epigenetic aspects of neuroblastoma heterogeneity. In addition, we summarize the recent findings on three crucial factors that can lead to heterogeneity in solid tumors: the inherent diversity of the progenitor cells, the presence of cancer stem cells, and the influence of the tumor microenvironment.
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Affiliation(s)
- Roshna Lawrence Gomez
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, United Arab Emirates
| | - Shakhzada Ibragimova
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, United Arab Emirates
| | - Revathy Ramachandran
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, United Arab Emirates
| | - Anna Philpott
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Center, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Fahad R Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, United Arab Emirates.
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33
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Zeineldin M, Patel AG, Dyer MA. Neuroblastoma: When differentiation goes awry. Neuron 2022; 110:2916-2928. [PMID: 35985323 PMCID: PMC9509448 DOI: 10.1016/j.neuron.2022.07.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 04/21/2022] [Accepted: 07/13/2022] [Indexed: 10/15/2022]
Abstract
Neuroblastoma is a leading cause of cancer-related death in children. Accumulated data suggest that differentiation arrest of the neural-crest-derived sympathoadrenal lineage contributes to neuroblastoma formation. The developmental arrest of these cell types explains many biological features of the disease, including its cellular heterogeneity, mutational spectrum, spontaneous regression, and response to drugs that induce tumor cell differentiation. In this review, we provide evidence that supports the notion that arrested neural-crest-derived progenitor cells give rise to neuroblastoma and discuss how this concept could be exploited for clinical management of the disease.
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Affiliation(s)
- Maged Zeineldin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Anand G Patel
- Departments of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, MS-323, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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34
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Precise identification of cancer cells from allelic imbalances in single cell transcriptomes. Commun Biol 2022; 5:884. [PMID: 36071103 PMCID: PMC9452529 DOI: 10.1038/s42003-022-03808-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/05/2022] [Indexed: 01/08/2023] Open
Abstract
A fundamental step of tumour single cell mRNA analysis is separating cancer and non-cancer cells. We show that the common approach to separation, using shifts in average expression, can lead to erroneous biological conclusions. By contrast, allelic imbalances representing copy number changes directly detect the cancer genotype and accurately separate cancer from non-cancer cells. Our findings provide a definitive approach to identifying cancer cells from single cell mRNA sequencing data. The identification of cancer cells from single cell transcriptomes can be improved by detecting allelic imbalances due to copy number changes.
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35
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Yu EY, Cheung NKV, Lue NF. Connecting telomere maintenance and regulation to the developmental origin and differentiation states of neuroblastoma tumor cells. J Hematol Oncol 2022; 15:117. [PMID: 36030273 PMCID: PMC9420296 DOI: 10.1186/s13045-022-01337-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/28/2022] [Indexed: 11/18/2022] Open
Abstract
A cardinal feature that distinguishes clinically high-risk neuroblastoma from low-risk tumors is telomere maintenance. Specifically, neuroblastoma tumors with either active telomerase or alternative lengthening of telomeres exhibit aggressive growth characteristics that lead to poor outcomes, whereas tumors without telomere maintenance can be managed with observation or minimal treatment. Even though the need for cancer cells to maintain telomere DNA-in order to sustain cell proliferation-is well established, recent studies suggest that the neural crest origin of neuroblastoma may enforce unique relationships between telomeres and tumor malignancy. Specifically in neuroblastoma, telomere structure and telomerase activity are correlated with the adrenergic/mesenchymal differentiation states, and manipulating telomerase activity can trigger tumor cell differentiation. Both findings may reflect features of normal neural crest development. This review summarizes recent advances in the characterization of telomere structure and telomere maintenance mechanisms in neuroblastoma and discusses the findings in the context of relevant literature on telomeres during embryonic and neural development. Understanding the canonical and non-canonical roles of telomere maintenance in neuroblastoma could reveal vulnerabilities for telomere-directed therapies with potential applications to other pediatric malignancies.
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Affiliation(s)
- Eun Young Yu
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Nai-Kong V Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Neal F Lue
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA.
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36
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Brazda P, Ruiz-Moreno C, Megchelenbrink WL, Timmers HJLM, Stunnenberg HG. Extensive patient-to-patient single nucleus transcriptome heterogeneity in pheochromocytomas and paragangliomas. Front Oncol 2022; 12:965168. [PMID: 36046044 PMCID: PMC9421253 DOI: 10.3389/fonc.2022.965168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Pheochromocytoma, neuroendocrine tumor, single cell RNA-sequencing, transcriptome, heterogeneity, SDHB, RET, paraganglinoma; Pheochromocytomas (PC) and paragangliomas (PG) are rare neuroendocrine tumors with varied genetic makeup and are associated with high cardiovascular morbidity and a variable risk of malignancy. The source of the transcriptional heterogeneity of the disease and the underlying biological processes that determine the outcome of PCPG remain largely unclear. We focused on PCPG tumors with germline SDHB and RET mutations, which represent distinct prognostic groups with worse or better prognoses, respectively. We applied single-nuclei RNA sequencing (snRNA-seq) to tissue samples from 11 patients and found high patient-to-patient transcriptome heterogeneity in neuroendocrine tumor cells. The tumor microenvironment also showed heterogeneous profiles, mainly contributed by macrophages of the immune cell clusters and Schwann cells of the stroma. By performing non-negative matrix factorization, we identified common transcriptional programs active in RET and SDHB, as well as distinct modules, including neuronal development, hormone synthesis and secretion, and DNA replication. Similarities between the transcriptomes of the tumor cells and those of the chromaffin- and precursor cell types suggests different developmental stages at which PC and PG tumors appear to be arrested.
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Affiliation(s)
- Peter Brazda
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Cristian Ruiz-Moreno
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Wout L. Megchelenbrink
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Henri J. L. M. Timmers
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hendrik G. Stunnenberg
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
- *Correspondence: Hendrik G. Stunnenberg,
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Gonzalez Malagon SG, Liu KJ. Linking neural crest development to neuroblastoma pathology. Development 2022; 149:276149. [DOI: 10.1242/dev.200331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Although rare, childhood (paediatric) cancers are a major cause of death in young children. Unlike many adult cancers, paediatric cancers, such as neuroblastoma (NB), are developmental diseases that rarely show genetic predispositions. NB is the most common extracranial solid tumour in children, accounting for ∼15% of paediatric cancer deaths. This heterogeneous cancer arises from undifferentiated neural crest-derived progenitor cells. As neural crest cells are multipotent and migratory, they are often considered the embryonic paradigm of cancer stem cells. However, very little is known about the events that trigger tumour initiation and progression. Here, we discuss recent insights into sympathoadrenal lineage specification, as well as genetic factors associated with NB. With this in mind, we consider the molecular underpinnings of NB in the context of developmental trajectories of the neural crest lineage. This allows us to compare distinct subtypes of the disease and gene-function interactions during sensitive phases of neural crest development.
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Affiliation(s)
- Sandra Guadalupe Gonzalez Malagon
- Biomedical Research Institute, Foundation for Research and Technology, University of Ioannina Campus 1 , 45115 Ioannina , Greece
- School of Health Sciences and Institute of Biosciences, University Research Centre, University of Ioannina 2 Department of Biological Applications and Technology , , 45110 Ioannina , Greece
| | - Karen J. Liu
- Centre for Craniofacial and Regenerative Biology, King's College London 3 , London SE1 9RT , UK
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Sainero-Alcolado L, Mushtaq M, Liaño-Pons J, Rodriguez-Garcia A, Yuan Y, Liu T, Ruiz-Pérez MV, Schlisio S, Bedoya-Reina O, Arsenian-Henriksson M. Expression and activation of nuclear hormone receptors result in neuronal differentiation and favorable prognosis in neuroblastoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:226. [PMID: 35850708 PMCID: PMC9295514 DOI: 10.1186/s13046-022-02399-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 05/19/2022] [Indexed: 01/20/2023]
Abstract
BACKGROUND Neuroblastoma (NB), a childhood tumor derived from the sympathetic nervous system, presents with heterogeneous clinical behavior. While some tumors regress spontaneously without medical intervention, others are resistant to therapy, associated with an aggressive phenotype. MYCN-amplification, frequently occurring in high-risk NB, is correlated with an undifferentiated phenotype and poor prognosis. Differentiation induction has been proposed as a therapeutic approach for high-risk NB. We have previously shown that MYCN maintains an undifferentiated state via regulation of the miR-17 ~ 92 microRNA cluster, repressing the nuclear hormone receptors (NHRs) estrogen receptor alpha (ERα) and the glucocorticoid receptor (GR). METHODS Cell viability was determined by WST-1. Expression of differentiation markers was analyzed by Western blot, RT-qPCR, and immunofluorescence analysis. Metabolic phenotypes were studied using Agilent Extracellular Flux Analyzer, and accumulation of lipid droplets by Nile Red staining. Expression of angiogenesis, proliferation, and neuronal differentiation markers, and tumor sections were assessed by immunohistochemistry. Gene expression from NB patient as well as adrenal gland cohorts were analyzed using GraphPad Prism software (v.8) and GSEA (v4.0.3), while pseudo-time progression on post-natal adrenal gland cells from single-nuclei transcriptome data was computed using scVelo. RESULTS Here, we show that simultaneous activation of GR and ERα potentiated induction of neuronal differentiation, reduced NB cell viability in vitro, and decreased tumor burden in vivo. This was accompanied by a metabolic reprogramming manifested by changes in the glycolytic and mitochondrial functions and in lipid droplet accumulation. Activation of the retinoic acid receptor alpha (RARα) with all-trans retinoic acid (ATRA) further enhanced the differentiated phenotype as well as the metabolic switch. Single-cell nuclei transcriptome analysis of human adrenal glands indicated a sequential expression of ERα, GR, and RARα during development from progenitor to differentiated chromaffin cells. Further, in silico analysis revealed that patients with higher combined expression of GR, ERα, and RARα mRNA levels had elevated expression of neuronal differentiation markers and a favorable outcome. CONCLUSION Together, our findings suggest that combination therapy involving activation of several NHRs could be a promising pharmacological approach for differentiation treatment of NB patients.
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Affiliation(s)
- Lourdes Sainero-Alcolado
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Muhammad Mushtaq
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 65 Stockholm, Sweden ,grid.440526.10000 0004 0609 3164Present address: Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, 87300 Pakistan
| | - Judit Liaño-Pons
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Aida Rodriguez-Garcia
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Ye Yuan
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Tong Liu
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 65 Stockholm, Sweden ,grid.4714.60000 0004 1937 0626Present address: Department of Medicine, Center for Molecular Medicine (CMM), Karolinska Institutet, SE-171 64 Stockholm, Sweden
| | - María Victoria Ruiz-Pérez
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Susanne Schlisio
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Oscar Bedoya-Reina
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 65 Stockholm, Sweden
| | - Marie Arsenian-Henriksson
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 65 Stockholm, Sweden
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Verhoeven BM, Mei S, Olsen TK, Gustafsson K, Valind A, Lindström A, Gisselsson D, Fard SS, Hagerling C, Kharchenko PV, Kogner P, Johnsen JI, Baryawno N. The immune cell atlas of human neuroblastoma. Cell Rep Med 2022; 3:100657. [PMID: 35688160 PMCID: PMC9245004 DOI: 10.1016/j.xcrm.2022.100657] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 01/26/2022] [Accepted: 05/17/2022] [Indexed: 12/03/2022]
Abstract
Understanding the complete immune cell composition of human neuroblastoma (NB) is crucial for the development of immunotherapeutics. Here, we perform single-cell RNA sequencing (scRNA-seq) on 19 human NB samples coupled with multiplex immunohistochemistry, survival analysis, and comparison with normal fetal adrenal gland data. We provide a comprehensive immune cell landscape and characterize cell-state changes from normal tissue to NB. Our analysis reveals 27 immune cell subtypes, including distinct subpopulations of myeloid, NK, B, and T cells. Several different cell types demonstrate a survival benefit. In contrast to adult cancers and previous NB studies, we show an increase in inflammatory monocyte cell state when contrasting normal and tumor tissue, while no differences in cytotoxicity and exhaustion score for T cells, nor in Treg activity, are observed. Our receptor-ligand interaction analysis reveals a highly complex interactive network of the NB microenvironment from which we highlight several interactions that we suggest for future therapeutic studies. 27 different immune subtypes form a complex neuroblastoma microenvironment Inflammatory monocytes correlate with neuroblastoma disease progression Active NK cells correlate with improved survival in human neuroblastoma T cell exhaustion and Treg activity demonstrate no difference between risk groups
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Affiliation(s)
- Bronte Manouk Verhoeven
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Shenglin Mei
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Thale Kristin Olsen
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Karin Gustafsson
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Anders Valind
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, 221 85 Lund, Sweden; Department of Pediatrics, Skåne University Hospital, Lund, Sweden
| | - Axel Lindström
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, 221 85 Lund, Sweden
| | - David Gisselsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, 221 85 Lund, Sweden
| | - Shahrzad Shirazi Fard
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Catharina Hagerling
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, 221 85 Lund, Sweden
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Per Kogner
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - John Inge Johnsen
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ninib Baryawno
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden.
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40
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Cellular plasticity in the neural crest and cancer. Curr Opin Genet Dev 2022; 75:101928. [PMID: 35749971 DOI: 10.1016/j.gde.2022.101928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/24/2022]
Abstract
In vertebrates, neural crest cells (NCCs) are a multipotent embryonic population generating both neural/neuronal and mesenchymal derivatives, and thus the neural crest (NC) is often referred to as the fourth germ layer. NC development is a dynamic process, where NCCs possess substantial plasticity in transcriptional and epigenomic profiles. Recent technical advances in single-cell and low-input sequencing have empowered fine-resolution characterisation of NC development. In this review, we summarise the latest models underlying NC-plasticity acquirement and cell-fate restriction, outline the connections between NC plasticity and NC-derived cancer and envision the new opportunities in studying NC plasticity and its link to cancer.
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41
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The need for a standard for informed consent for collection of human fetal material. Stem Cell Reports 2022; 17:1245-1247. [PMID: 35705013 PMCID: PMC9214061 DOI: 10.1016/j.stemcr.2022.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
The ISSCR has developed the Informed Consent Standards for Human Fetal Tissue Donation and Research to promote uniformity and transparency in tissue donation and collection. This standard is designed to assist those working with and overseeing the regulation of such tissue and reassure the wider community and public.
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42
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BET and CDK Inhibition Reveal Differences in the Proliferation Control of Sympathetic Ganglion Neuroblasts and Adrenal Chromaffin Cells. Cancers (Basel) 2022; 14:cancers14112755. [PMID: 35681734 PMCID: PMC9179499 DOI: 10.3390/cancers14112755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 01/09/2023] Open
Abstract
Neuroblastoma arising from the adrenal differ from ganglionic neuroblastoma both genetically and clinically, with adrenal tumors being associated with a more severe prognosis. The different tumor properties may be linked to specific tumor founder cells in adrenal and sympathetic ganglia. To address this question, we first set up cultures of mouse sympathetic neuroblasts and adrenal chromaffin cells. These cultures were then treated with various proliferation inhibitors to identify lineage-specific responses. We show that neuroblast and chromaffin cell proliferation was affected by WNT, ALK, IGF1, and PRC2/EZH2 signaling inhibitors to a similar extent. However, differential effects were observed in response to bromodomain and extraterminal (BET) protein inhibitors (JQ1, GSK1324726A) and to the CDK-7 inhibitor THZ1, with BET inhibitors preferentially affecting chromaffin cells, and THZ1 preferentially affecting neuroblasts. The differential dependence of chromaffin cells and neuroblasts on BET and CDK signaling may indicate different mechanisms during tumor initiation in sympathetic ganglia and adrenal.
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43
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Dohmen J, Baranovskii A, Ronen J, Uyar B, Franke V, Akalin A. Identifying tumor cells at the single-cell level using machine learning. Genome Biol 2022; 23:123. [PMID: 35637521 PMCID: PMC9150321 DOI: 10.1186/s13059-022-02683-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/06/2022] [Indexed: 12/15/2022] Open
Abstract
Tumors are complex tissues of cancerous cells surrounded by a heterogeneous cellular microenvironment with which they interact. Single-cell sequencing enables molecular characterization of single cells within the tumor. However, cell annotation—the assignment of cell type or cell state to each sequenced cell—is a challenge, especially identifying tumor cells within single-cell or spatial sequencing experiments. Here, we propose ikarus, a machine learning pipeline aimed at distinguishing tumor cells from normal cells at the single-cell level. We test ikarus on multiple single-cell datasets, showing that it achieves high sensitivity and specificity in multiple experimental contexts.
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Affiliation(s)
- Jan Dohmen
- Bioinformatics and Omics Data Science Platform, Berlin Institute For Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Hannoversche Str.28, 10115, Berlin, Germany
| | - Artem Baranovskii
- Non-coding RNAs and Mechanisms of Cytoplasmic Gene Regulation Lab, Berlin Institute for Medical Systems Biology, Hannoversche Str. 28, 10115, Berlin, Germany.,Free University Berlin, Kaiserswerther Str. 16-18, 14195, Berlin, Germany
| | - Jonathan Ronen
- Bioinformatics and Omics Data Science Platform, Berlin Institute For Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Hannoversche Str.28, 10115, Berlin, Germany
| | - Bora Uyar
- Bioinformatics and Omics Data Science Platform, Berlin Institute For Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Hannoversche Str.28, 10115, Berlin, Germany
| | - Vedran Franke
- Bioinformatics and Omics Data Science Platform, Berlin Institute For Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Hannoversche Str.28, 10115, Berlin, Germany.
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute For Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Hannoversche Str.28, 10115, Berlin, Germany.
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Abstract
Neuroblastomas are tumours of sympathetic origin, with a heterogeneous clinical course ranging from localized or spontaneously regressing to widely metastatic disease. Neuroblastomas recapitulate many of the features of sympathoadrenal development, which have been directly targeted to improve the survival outcomes in patients with high-risk disease. Over the past few decades, improvements in the 5-year survival of patients with metastatic neuroblastomas, from <20% to >50%, have resulted from clinical trials incorporating high-dose chemotherapy with autologous stem cell transplantation, differentiating agents and immunotherapy with anti-GD2 monoclonal antibodies. The next generation of trials are designed to improve the initial response rates in patients with high-risk neuroblastomas via the addition of immunotherapies, targeted therapies (such as ALK inhibitors) and radiopharmaceuticals to standard induction regimens. Other trials are focused on testing precision medicine strategies for patients with relapsed and/or refractory disease, enhancing the antitumour immune response and improving the effectiveness of maintenance regimens, in order to prolong disease remission. In this Review, we describe advances in delineating the pathogenesis of neuroblastoma and in identifying the drivers of high-risk disease. We then discuss how this knowledge has informed improvements in risk stratification, risk-adapted therapy and the development of novel therapies.
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45
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McNerney KO, Karageorgos S, Ferry GM, Wolpaw AJ, Burudpakdee C, Khurana P, Toland CN, Vemu R, Vu A, Hogarty MD, Bassiri H. TH-MYCN tumors, but not tumor-derived cell lines, are adrenergic lineage, GD2+, and responsive to anti-GD2 antibody therapy. Oncoimmunology 2022; 11:2075204. [PMID: 35646475 PMCID: PMC9132414 DOI: 10.1080/2162402x.2022.2075204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Neuroblastoma is a commonly lethal solid tumor of childhood and intensive chemoradiotherapy treatment cures ~50% of children with high-risk disease. The addition of immunotherapy using dinutuximab, a monoclonal antibody directed against the GD2 disialoganglioside expressed on neuroblasts, improves survival when incorporated into front-line therapy and shows robust activity in regressing relapsed disease when combined with chemotherapy. Still, many children succumb to neuroblastoma progression despite receiving dinutuximab-based immunotherapy, and efforts to counteract the immune suppressive signals responsible are warranted. Animal models of human cancers provide useful platforms to study immunotherapies. TH-MYCN transgenic mice are immunocompetent and develop neuroblastomas at autochthonous sites due to enforced MYCN expression in developing neural crest tissues. However, GD2-directed immunotherapy in this model has been underutilized due to the prevailing notion that TH-MYCN neuroblasts express insufficient GD2 to be targeted. We demonstrate that neuroblasts in TH-MYCN-driven tumors express GD2 at levels comparable to human neuroblastomas but rapidly lose GD2 expression when explanted ex vivo to establish tumor cell lines. This occurs in association with a transition from an adrenergic to mesenchymal differentiation state. Importantly, not only is GD2 expression retained on tumors in situ, treatment with a murine anti-GD2 antibody, 14G2a, markedly extends survival in such mice, including durable complete responses. Tumors in 14G2a-treated mice have fewer macrophage and myeloid-derived suppressor cells in their tumor microenvironment. Our findings support the utility of this model to inform immunotherapy approaches for neuroblastoma and potential opportunities to investigate drivers of adrenergic to mesenchymal fate decisions.
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Affiliation(s)
- KO McNerney
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - S Karageorgos
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - GM Ferry
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - AJ Wolpaw
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- The Wistar Institute, Philadelphia, PA
| | - C Burudpakdee
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - P Khurana
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - CN Toland
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - R Vemu
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - A Vu
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - MD Hogarty
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - H Bassiri
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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46
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Shendy NAM, Zimmerman MW, Abraham BJ, Durbin AD. Intrinsic transcriptional heterogeneity in neuroblastoma guides mechanistic and therapeutic insights. Cell Rep Med 2022; 3:100632. [PMID: 35584622 PMCID: PMC9133465 DOI: 10.1016/j.xcrm.2022.100632] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/24/2022] [Accepted: 04/20/2022] [Indexed: 12/20/2022]
Abstract
Cell state is controlled by master transcription factors (mTFs) that determine the cellular gene expression program. Cancer cells acquire dysregulated gene expression programs by mutational and non-mutational processes. Intratumoral heterogeneity can result from cells displaying distinct mTF-regulated cell states, which co-exist within the tumor. One archetypal tumor associated with transcriptionally regulated heterogeneity is high-risk neuroblastoma (NB). Patients with NB have poor overall survival despite intensive therapies, and relapsed patients are commonly refractory to treatment. The cellular populations that comprise NB are marked by different cohorts of mTFs and differential sensitivity to conventional therapies. Recent studies have highlighted mechanisms by which NB cells dynamically shift the cell state with treatment, revealing new opportunities to control the cellular response to treatment by manipulating cell-state-defining transcriptional programs. Here, we review recent advances in understanding transcriptionally defined cancer heterogeneity. We offer challenges to the field to encourage translation of basic science into clinical benefit.
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Affiliation(s)
- Noha A M Shendy
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mark W Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Brian J Abraham
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Adam D Durbin
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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47
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Ben Amar D, Thoinet K, Villalard B, Imbaud O, Costechareyre C, Jarrosson L, Reynaud F, Novion Ducassou J, Couté Y, Brunet JF, Combaret V, Corradini N, Delloye-Bourgeois C, Castellani V. Environmental cues from neural crest derivatives act as metastatic triggers in an embryonic neuroblastoma model. Nat Commun 2022; 13:2549. [PMID: 35538114 PMCID: PMC9091272 DOI: 10.1038/s41467-022-30237-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 04/21/2022] [Indexed: 12/04/2022] Open
Abstract
Embryonic malignant transformation is concomitant to organogenesis, often affecting multipotent and migratory progenitors. While lineage relationships between malignant cells and their physiological counterparts are extensively investigated, the contribution of exogenous embryonic signals is not fully known. Neuroblastoma (NB) is a childhood malignancy of the peripheral nervous system arising from the embryonic trunk neural crest (NC) and characterized by heterogeneous and interconvertible tumor cell identities. Here, using experimental models mimicking the embryonic context coupled to proteomic and transcriptomic analyses, we show that signals released by embryonic sympathetic ganglia, including Olfactomedin-1, induce NB cells to shift from a noradrenergic to mesenchymal identity, and to activate a gene program promoting NB metastatic onset and dissemination. From this gene program, we extract a core signature specifically shared by metastatic cancers with NC origin. This reveals non-cell autonomous embryonic contributions regulating the plasticity of NB identities and setting pro-dissemination gene programs common to NC-derived cancers.
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Affiliation(s)
- Dounia Ben Amar
- University of Lyon, University Claude Bernard Lyon 1, MeLiS, CNRS UMR5284, INSERM U1314, NeuroMyoGene Institute, 69008, Lyon, France, 8 avenue Rockefeller
| | - Karine Thoinet
- University of Lyon, University Claude Bernard Lyon 1, MeLiS, CNRS UMR5284, INSERM U1314, NeuroMyoGene Institute, 69008, Lyon, France, 8 avenue Rockefeller
| | - Benjamin Villalard
- University of Lyon, University Claude Bernard Lyon 1, MeLiS, CNRS UMR5284, INSERM U1314, NeuroMyoGene Institute, 69008, Lyon, France, 8 avenue Rockefeller
| | - Olivier Imbaud
- University of Lyon, University Claude Bernard Lyon 1, MeLiS, CNRS UMR5284, INSERM U1314, NeuroMyoGene Institute, 69008, Lyon, France, 8 avenue Rockefeller
| | | | | | - Florie Reynaud
- University of Lyon, University Claude Bernard Lyon 1, MeLiS, CNRS UMR5284, INSERM U1314, NeuroMyoGene Institute, 69008, Lyon, France, 8 avenue Rockefeller
| | - Julia Novion Ducassou
- University Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048 38000, Grenoble, France
| | - Yohann Couté
- University Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048 38000, Grenoble, France
| | - Jean-François Brunet
- Institut de Biologie de l'ENS (IBENS), Inserm, CNRS, École normale supérieure, PSL Research University, Paris, France
| | - Valérie Combaret
- Laboratory of Translational Research, Léon Bérard Centre, Lyon, France
| | - Nadège Corradini
- Departments of Oncology and Clinical Research, Centre Léon Berard and Institut d'Hématologie et d'Oncologie Pédiatrique, Lyon, France
| | - Céline Delloye-Bourgeois
- University of Lyon, University Claude Bernard Lyon 1, MeLiS, CNRS UMR5284, INSERM U1314, NeuroMyoGene Institute, 69008, Lyon, France, 8 avenue Rockefeller.
| | - Valérie Castellani
- University of Lyon, University Claude Bernard Lyon 1, MeLiS, CNRS UMR5284, INSERM U1314, NeuroMyoGene Institute, 69008, Lyon, France, 8 avenue Rockefeller.
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48
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Khabirova E, Jardine L, Coorens THH, Webb S, Treger TD, Engelbert J, Porter T, Prigmore E, Collord G, Piapi A, Teichmann SA, Inglott S, Williams O, Heidenreich O, Young MD, Straathof K, Bomken S, Bartram J, Haniffa M, Behjati S. Single-cell transcriptomics reveals a distinct developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia. Nat Med 2022; 28:743-751. [PMID: 35288693 PMCID: PMC9018413 DOI: 10.1038/s41591-022-01720-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/27/2022] [Indexed: 12/23/2022]
Abstract
KMT2A-rearranged infant ALL is an aggressive childhood leukemia with poor prognosis. Here, we investigated the developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia (B-ALL) using bulk messenger RNA (mRNA) meta-analysis and examination of single lymphoblast transcriptomes against a developing bone marrow reference. KMT2A-rearranged infant B-ALL was uniquely dominated by an early lymphocyte precursor (ELP) state, whereas less adverse NUTM1-rearranged infant ALL demonstrated signals of later developing B cells, in line with most other childhood B-ALLs. We compared infant lymphoblasts with ELP cells and revealed that the cancer harbored hybrid myeloid-lymphoid features, including nonphysiological antigen combinations potentially targetable to achieve cancer specificity. We validated surface coexpression of exemplar combinations by flow cytometry. Through analysis of shared mutations in separate leukemias from a child with infant KMT2A-rearranged B-ALL relapsing as AML, we established that KMT2A rearrangement occurred in very early development, before hematopoietic specification, emphasizing that cell of origin cannot be inferred from the transcriptional state.
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Affiliation(s)
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Haematology Department, Freeman Hospital, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Simone Webb
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Taryn D Treger
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Grace Collord
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, University College London Hospital, London, UK
- Department of Haematology, University College London Cancer Institute, London, UK
| | - Alice Piapi
- Great Ormond Street Hospital for Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | | | - Sarah Inglott
- Great Ormond Street Hospital for Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - Owen Williams
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Olaf Heidenreich
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Karin Straathof
- Great Ormond Street Hospital for Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Simon Bomken
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
- The Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | - Jack Bartram
- Great Ormond Street Hospital for Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK.
- UCL Great Ormond Street Institute of Child Health, London, UK.
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Hinxton, UK.
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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49
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Abstract
Purpose of Review The evolving information of the initiation, tumor cell heterogeneity, and plasticity of childhood neuroblastoma has opened up new perspectives for developing therapies based on detailed knowledge of the disease. Recent Findings The cellular origin of neuroblastoma has begun to unravel and there have been several reports on tumor cell heterogeneity based on transcriptional core regulatory circuitries that have given us important information on the biology of neuroblastoma as a developmental disease. This together with new insight of the tumor microenvironment which acts as a support for neuroblastoma growth has given us the prospect for designing better treatment approaches for patients with high-risk neuroblastoma. Here, we discuss these new discoveries and highlight some emerging therapeutic options. Summary Neuroblastoma is a disease with multiple facets. Detailed biological and molecular knowledge on neuroblastoma initiation, heterogeneity, and the communications between cells in the tumor microenvironment holds promise for better therapies.
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50
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Ponzoni M, Bachetti T, Corrias MV, Brignole C, Pastorino F, Calarco E, Bensa V, Giusto E, Ceccherini I, Perri P. Recent advances in the developmental origin of neuroblastoma: an overview. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:92. [PMID: 35277192 PMCID: PMC8915499 DOI: 10.1186/s13046-022-02281-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 02/06/2022] [Indexed: 02/04/2023]
Abstract
Neuroblastoma (NB) is a pediatric tumor that originates from neural crest-derived cells undergoing a defective differentiation due to genomic and epigenetic impairments. Therefore, NB may arise at any final site reached by migrating neural crest cells (NCCs) and their progeny, preferentially in the adrenal medulla or in the para-spinal ganglia. NB shows a remarkable genetic heterogeneity including several chromosome/gene alterations and deregulated expression of key oncogenes that drive tumor initiation and promote disease progression. NB substantially contributes to childhood cancer mortality, with a survival rate of only 40% for high-risk patients suffering chemo-resistant relapse. Hence, NB remains a challenge in pediatric oncology and the need of designing new therapies targeted to specific genetic/epigenetic alterations become imperative to improve the outcome of high-risk NB patients with refractory disease or chemo-resistant relapse. In this review, we give a broad overview of the latest advances that have unraveled the developmental origin of NB and its complex epigenetic landscape. Single-cell RNA sequencing with spatial transcriptomics and lineage tracing have identified the NCC progeny involved in normal development and in NB oncogenesis, revealing that adrenal NB cells transcriptionally resemble immature neuroblasts or their closest progenitors. The comparison of adrenal NB cells from patients classified into risk subgroups with normal sympatho-adrenal cells has highlighted that tumor phenotype severity correlates with neuroblast differentiation grade. Transcriptional profiling of NB tumors has identified two cell identities that represent divergent differentiation states, i.e. undifferentiated mesenchymal (MES) and committed adrenergic (ADRN), able to interconvert by epigenetic reprogramming and to confer intra-tumoral heterogeneity and high plasticity to NB. Chromatin immunoprecipitation sequencing has disclosed the existence of two super-enhancers and their associated transcription factor networks underlying MES and ADRN identities and controlling NB gene expression programs. The discovery of NB-specific regulatory circuitries driving oncogenic transformation and maintaining the malignant state opens new perspectives on the design of innovative therapies targeted to the genetic and epigenetic determinants of NB. Remodeling the disrupted regulatory networks from a dysregulated expression, which blocks differentiation and enhances proliferation, toward a controlled expression that prompts the most differentiated state may represent a promising therapeutic strategy for NB.
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Affiliation(s)
- Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Tiziana Bachetti
- U.O. Proteomica e Spettrometria di Massa, IRCSS Ospedale Policlinico San Martino, Genoa, Italy
| | - Maria Valeria Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Chiara Brignole
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Fabio Pastorino
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Enzo Calarco
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Veronica Bensa
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Elena Giusto
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy
| | - Isabella Ceccherini
- Laboratory of Genetics and Genomics of Rare Diseases, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Patrizia Perri
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147, Genoa, Italy.
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